[med-svn] [python-mne] 195/376: fixing manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:35 UTC 2015
This is an automated email from the git hooks/post-receive script.
yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 018c573bcb233ba00286121dd1d1c48c874d1a5f
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Thu Apr 14 16:37:18 2011 -0400
fixing manual
---
doc/source/manual/AppA.rst | 48 ++---
doc/source/manual/AppB.rst | 34 ++--
doc/source/manual/AppInstall.rst | 22 +--
doc/source/manual/analyze.rst | 58 +++---
doc/source/manual/browse.rst | 385 +++++++++++++++++++--------------------
doc/source/manual/convert.rst | 344 +++++++++++++++++-----------------
doc/source/manual/cookbook.rst | 148 +++++++--------
doc/source/manual/forward.rst | 126 ++++++-------
doc/source/manual/intro.rst | 2 +-
doc/source/manual/list.rst | 12 +-
doc/source/manual/matlab.rst | 4 +-
doc/source/manual/mne.rst | 186 +++++++++----------
doc/source/manual/morph.rst | 44 ++---
doc/source/manual/sampledata.rst | 22 +--
doc/source/manual/utilities.rst | 152 ++++++++--------
15 files changed, 793 insertions(+), 794 deletions(-)
diff --git a/doc/source/manual/AppA.rst b/doc/source/manual/AppA.rst
index 5abd27a..b250df7 100755
--- a/doc/source/manual/AppA.rst
+++ b/doc/source/manual/AppA.rst
@@ -17,7 +17,7 @@ The name of the program is mri_watershed .
Its use in the MNE environment is facilitated by the script mne_watershed_bem ,
which assumes the following options:
-**\---subject <subject>**
+**\---subject <*subject*>**
Defines the name of the subject. This can be also accomplished
by setting the SUBJECT environment variable.
@@ -34,26 +34,26 @@ which assumes the following options:
After mne_watershed_bem has
completed, the following files appear in the subject's ``bem/watershed`` directory:
-**<subject> _brain_surface**
+** <*subject*> _brain_surface**
Contains the brain surface triangulation.
-**<subject> _inner_skull_surface**
+** <*subject*> _inner_skull_surface**
Contains the inner skull triangulation.
-**<subject> _outer_skull_surface**
+** <*subject*> _outer_skull_surface**
Contains the outer skull triangulation.
-**<subject> _outer_skin_surface**
+** <*subject*> _outer_skin_surface**
Contains the scalp triangulation.
All of these surfaces are in the FreeSurfer format. In addition,
there will be a directory called ``bem/watershed/ws`` which
contains the brain MRI volume. Furthermore, mne_watershed_bem script
-converts the scalp surface to fif format and saves the result to ``bem/`` <subject> ``-head.fif`` . The mne_analyze tool
+converts the scalp surface to fif format and saves the result to ``bem/`` <*subject*> ``-head.fif`` . The mne_analyze tool
described :ref:`ch_interactive_analysis` looks for this file the visualizations
involving the scalp surface.
@@ -105,23 +105,23 @@ proceed as follows:
- Copy all of your images or create symbolic
links to them in a single directory. The images must be in DICOM
- format. We will refer to this directory as <source> .
+ format. We will refer to this directory as <*source*> .
- Create another directory to hold the output of mne_organize_dicom . We
- will refer to this directory as <dest> .
+ will refer to this directory as <*dest*> .
-- Change the working directory to <dest> .
+- Change the working directory to <*dest*> .
-- Say ``mne_organize_dicom`` <source> .
- Depending on the total number of images in <source> this
+- Say ``mne_organize_dicom`` <*source*> .
+ Depending on the total number of images in <*source*> this
script may take quite a while to run. Progress is indicated by
listing the number of images processed at 50-image intervals.
-As a result, <dest> will
-contain several directories named <three-digit number> _<protocol_name> corresponding
+As a result, <*dest*> will
+contain several directories named <*three-digit number*> _ <*protocol_name*> corresponding
to the different series of images acquired. Spaces and parenthesis
in protocol names will be replaced by underscores. Under each of
-these directories there are one or more directories named <three-digit> number
+these directories there are one or more directories named <*three-digit*> number
corresponding to one or more subsets of images in this series (protocol).
The only subset division scheme implemented in mne_organize_dicom is
that according to different echoes, typically found in multi-echo
@@ -160,9 +160,9 @@ already in place. The following options can be specified:
The 30-degree flip angle data are not used.
-**\---unwarp <type>**
+**\---unwarp <*type*>**
- Run grad_unwarp with ``--unwarp`` <type> option on each of the converted
+ Run grad_unwarp with ``--unwarp`` <*type*> option on each of the converted
data sets.
Before running mne_flash_bem do
@@ -171,16 +171,16 @@ the following:
- Run mne_organize_dicom as
described above.
-- Change to the <dest> directory
+- Change to the <*dest*> directory
where mne_organize_dicom created the
image directory structure.
- Create symbolic links from the directories containing the
5-degree and 30-degree flip angle FLASH series to ``flash05`` and ``flash30`` , respectively:
- - ``ln -s`` <FLASH 5 series dir> ``flash05``
+ - ``ln -s`` <*FLASH 5 series dir*> ``flash05``
- - ``ln -s`` <FLASH 30 series dir> ``flash30``
+ - ``ln -s`` <*FLASH 30 series dir*> ``flash30``
- Set the ``SUBJECTS_DIR`` and ``SUBJECT`` environment
variables
@@ -193,10 +193,10 @@ The script encapsulates the following processing steps:
- It creates an mgz file corresponding
to each of the eight echoes in each of the FLASH directories in ``mri/flash`` .
- The files will be called ``mef`` <flip-angle> _<echo-number> ``.mgz`` .
+ The files will be called ``mef`` <*flip-angle*> _ <*echo-number*> ``.mgz`` .
- If the ``--unwarp`` option is specified, run grad_unwarp and produce
- files ``mef`` <flip-angle> _<echo-number> ``u.mgz`` .
+ files ``mef`` <*flip-angle*> _ <*echo-number*> ``u.mgz`` .
These files will be then used in the following steps.
- It creates parameter maps in ``mri/flash/parameter_maps`` using mri_ms_fitparms .
@@ -329,17 +329,17 @@ is:
Using the mri_convert utility
available in FreeSurfer , convert
an MRI volume to the img (Analyze) format. This volume should be the
- T1.mgz volume or a volume registered with T1.mgz in FreeSurfer :``mri_convert`` <volume> ``.mgz`` <volume> ``.img``
+ T1.mgz volume or a volume registered with T1.mgz in FreeSurfer :``mri_convert`` <*volume*> ``.mgz`` <*volume*> ``.img``
**Step 2**
- Transfer <volume> ``.mgz`` to
+ Transfer <*volume*> ``.mgz`` to
a location accessible to BrainSuite , running
on Windows.
**Step 3**
- Using <volume> ``.img`` as
+ Using <*volume*> ``.img`` as
input, create the tessellations of scalp, outer skull, and inner
skull surfaces in BrainSuite .
diff --git a/doc/source/manual/AppB.rst b/doc/source/manual/AppB.rst
index b77a749..1ef1f45 100755
--- a/doc/source/manual/AppB.rst
+++ b/doc/source/manual/AppB.rst
@@ -17,8 +17,8 @@ User environment
In the Martinos Center computer network, the 2.7 version
of MNE is located at /usr/pubsw/packages/mne/stable. To use this
version, follow :ref:`CIHCDHGI` substituting /usr/pubsw/packages/mne/stable
-for <MNE> and /usr/pubsw/packages/matlab/current
-for <Matlab> . For most users,
+for <*MNE*> and /usr/pubsw/packages/matlab/current
+for <*Matlab*> . For most users,
the default shell is tcsh.
.. note:: A new version of MNE is build every night from the latest sources. This version is located at /usr/pubsw/packages/mne/nightly.
@@ -142,31 +142,31 @@ the following command-line options:
List the command-line options.
-**\---inv <name>**
+**\---inv <*name*>**
Load the inverse operator decomposition from here.
-**\---meas <name>**
+**\---meas <*name*>**
Load the MEG or EEG data from this file.
-**\---set <number>**
+**\---set <*number*>**
The data set (condition) number to load. The list of data sets can
be seen, *e.g.*, in mne_analyze , mne_browse_raw ,
and xplotter .
-**\---bmin <time/ms>**
+**\---bmin <*time/ms*>**
Specifies the starting time of the baseline. In order to activate
baseline correction, both ``--bmin`` and ``--bmax`` options
must be present.
-**\---bmax <time/ms>**
+**\---bmax <*time/ms*>**
Specifies the finishing time of the baseline.
-**\---nave <value>**
+**\---nave <*value*>**
Specifies the number of averaged epochs in the input data. If the input
data file is one produced by mne_process_raw or mne_browse_raw ,
@@ -177,7 +177,7 @@ the following command-line options:
either by employing this flag or by adjusting the number of averages
in the data file with help of mne_change_nave .
-**\---snr <value>**
+**\---snr <*value*>**
An estimate for the amplitude SNR. The regularization parameter will
be set as INLINE_EQUATION. If the SNR option is
@@ -237,11 +237,11 @@ the following command-line options:
Output true current values in SI units (Am). By default, the currents are
scaled so that the maximum current value is set to 50 (Am).
-**\---out <name>**
+**\---out <*name*>**
Specifies the output file name. This is the 'stem' of
the output file name. The actual name is derived by removing anything up
- to and including the last period from the end of <name> .
+ to and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` or ``-rh`` is
then appended. Finally, ``.stc`` or ``.w`` is added,
depending on the output file type.
@@ -253,12 +253,12 @@ the following command-line options:
and dSPMs can be output as wfiles if one of the collapse options
is selected.
-**\---pred <name>**
+**\---pred <*name*>**
Save the predicted data into this file. This is a fif file containing
the predicted data waveforms, see :ref:`CHDCACDC`.
-**\---outputnorm <name>**
+**\---outputnorm <*name*>**
Output noise-normalization factors to this file.
@@ -267,7 +267,7 @@ the following command-line options:
Output inverse noise-normalization factors to the file defined by
the ``--outputnorm`` option.
-**\---dip <name>**
+**\---dip <*name*>**
Specifies a dipole distribution snapshot file. This is a file containing the
current distribution at a time specified with the ``--diptime`` option.
@@ -277,16 +277,16 @@ the following command-line options:
distribution. This option is only effective if the ``--spm`` option
is absent.
-**\---diptime <time/ms>**
+**\---diptime <*time/ms*>**
Time for the dipole snapshot, see ``--dip`` option above.
-**\---label <name>**
+**\---label <*name*>**
Label to process. The label files are produced by tksurfer and specify
regions of interests (ROIs). A label file name should end with ``-lh.label`` for
left-hemisphere ROIs and with ``-rh.label`` for right-hemisphere
- ones. The corresponding output files are tagged with ``-lh-`` <data type ``.amp`` and ``-rh-`` <data type ``.amp`` , respectively. <data type> equals ``MNE`` for expected current
+ ones. The corresponding output files are tagged with ``-lh-`` <*data type ``.amp`` and ``-rh-`` <*data type ``.amp`` , respectively. <*data type*> equals ``MNE`` for expected current
data and ``spm`` for dSPM data. Each line of the output
file contains the waveform of the output quantity at one of the
source locations falling inside the ROI.
diff --git a/doc/source/manual/AppInstall.rst b/doc/source/manual/AppInstall.rst
index be4759f..da2888b 100755
--- a/doc/source/manual/AppInstall.rst
+++ b/doc/source/manual/AppInstall.rst
@@ -37,14 +37,14 @@ Download the software
Download the software package of interest. The file names
follow the convention:
-MNE-*<version>*-<rev> -*<Operating
-system>*-*<Processor>*.*<ext>*
+MNE-* <*version*>*- <*rev*> -* <*Operating
+system*>*-* <*Processor*>*.* <*ext*>*
-The present version number is 2.7.0. The <rev> field
+The present version number is 2.7.0. The <*rev*> field
is the SVN revision number at the time this package was created.
-The <Operating system> field
-is either Linux or MacOSX. The <processor> field
-is either i386 or x86_64. The <ext> field
+The <*Operating system*> field
+is either Linux or MacOSX. The <*processor*> field
+is either i386 or x86_64. The <*ext*> field
is 'gz' for compressed tar archive files and 'dmg' for
Mac OSX disk images.
@@ -53,27 +53,27 @@ Installing from a compressed tar archive
Go to the directory where you want the software to be installed:
-``cd`` <dir>
+``cd`` <*dir*>
Unpack the tar archive:
-``tar zxvf`` <software package>
+``tar zxvf`` <*software package*>
-The name of the software directory under <dir> will
+The name of the software directory under <*dir*> will
be the same as the package file without the .gz extension.
Installing from a Mac OSX disk image
=====================================
- Double click on the disk image file.
- A window opens with the installer package (<name> .pkg)
+ A window opens with the installer package ( <*name*> .pkg)
inside.
- Double click the the package file. The installer starts.
- Follow the instructions in the installer.
-.. note:: The software will be installed to /Applications/<name> by default. If you want another location, select Choose Folder... on the Select a Destination screen in the installer.
+.. note:: The software will be installed to /Applications/ <*name*> by default. If you want another location, select Choose Folder... on the Select a Destination screen in the installer.
.. note:: To provide centralized support in an environment with
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index f55d578..f7bccaa 100755
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -67,21 +67,21 @@ options:
List the command-line options.
-**\---cd <dir>**
+**\---cd <*dir*>**
Change to this directory before starting.
-**\---subject <name>**
+**\---subject <*name*>**
Specify the default subject name for surface loading.
-**\---digtrig <name>**
+**\---digtrig <*name*>**
Name of the digital trigger channel. The default value is 'STI
014'. Underscores in the channel name will be replaced
by spaces.
-**\---digtrigmask <number>**
+**\---digtrigmask <*number*>**
Mask to be applied to the raw data trigger channel values before considering
them. This option is useful if one wants to set some bits in a don't
@@ -98,14 +98,14 @@ options:
Start mne_analyze in the restricted *head
position visualization* mode. For details, see :ref:`CHDEDFAE`.
-**\---dig <filename>**
+**\---dig <*filename*>**
Specify a file containing the head shape digitization data. This option
is only usable if the *head position visualization* position
visualization mode has been first invoked with the --visualizehpi
option.
-**\---hpi <filename>**
+**\---hpi <*filename*>**
Specify a file containing the transformation between the MEG device
and head coordinate frames. This option is only usable if the *head
@@ -436,7 +436,7 @@ dialog shown in :ref:`CACFHAIH` appears. It has four sections:
- MRI/head transform source specifies a file to read the MRI/MEG coordinate
transformation information from. This is usually the inverse operator
file. However, you can also load data with inverse operator set
- to <none> to view the data
+ to <*none*> to view the data
as well as field and potential maps derived thereof. In this case
you need to specify the coordinate transformation file using the Select... button,
usually located in ``mri/T1-neuromag/sets`` under the subject's
@@ -448,7 +448,7 @@ dialog shown in :ref:`CACFHAIH` appears. It has four sections:
- Use EEG average electrode ref. selects
whether the average electrode reference is applied to the data.
- This is only available if the inverse operator is set to <none> .
+ This is only available if the inverse operator is set to <*none*> .
- nave specifies the effective
number of averages to compute the SNR correctly. Usually your measurement
@@ -952,30 +952,30 @@ If the file ``$HOME/.mne/eyes`` exists, it is used instead.
All lines in the eyes file starting with # are comments.
The view orientation definition lines have the format:
-<name>:<Left>:<Right>:<Left up>:<Right up> ,
+<*name*>:<*Left*>:<*Right*>:<*Left up*>:<*Right up*> ,
where
-**<name>**
+**<*name*>**
is the name of this viewing orientation,
-**<Left>**
+**<*Left*>**
specifies the coordinates of the viewing 'eye' location
for the left hemisphere, separated by spaces,
-**<Right>**
+**<*Right*>**
specifies the coordinates of the viewing location for the right
hemisphere,
-**<Left up>**
+**<*Left up*>**
specifies the direction which is pointing up in the image for left hemisphere,
and
-**<Right up>**
+**<*Right up*>**
is the corresponding up vector for the right hemisphere.
@@ -1171,20 +1171,20 @@ selected, the following additional surfaces will be loaded:
- The BEM surfaces.
-The scalp surface is loaded from the file ``bem/`` <subject>``-head.fif`` under
+The scalp surface is loaded from the file ``bem/`` <*subject*>``-head.fif`` under
the subject's FreeSurfer directory. This surface is automatically
prepared if you use the watershed algorithm as described in :ref:`BABBDHAG`.
If you have another source for the head triangulation you can use
the utility mne_surf2bem to create
the fif format scalp surface file, see :ref:`BEHCACCJ`.
-If a file called ``bem/`` <subject>``-bem.fif`` under
+If a file called ``bem/`` <*subject*>``-bem.fif`` under
the subject's FreeSurfer directory is present, mne_analyze tries
to load the BEM surface triangulations from there. This file can
be a symbolic link to one of the ``-bem.files`` created
by mne_prepare_bem_model , see :ref:`CHDJFHEB`.
If the BEM file contains a head surface triangulation, it will be
-used instead of the one present in the ``bem/`` <subject>``-head.fif`` file.
+used instead of the one present in the ``bem/`` <*subject*>``-head.fif`` file.
Once all required surfaces have been loaded, the viewer window
shown in :ref:`CACJDFFH` pops up. In addition to the display
@@ -1716,7 +1716,7 @@ The labels provide means to interrogate timecourse information
from ROIs. The label files can be created in mne_analyze ,
see :ref:`CACJCFJJ` or in tksurfer ,
which is part of the FreeSurfer software. For mne_analyze left-hemisphere
-and right-hemisphere label files should be named <name> ``-lh.label`` and <name> ``-rh.label`` ,
+and right-hemisphere label files should be named <*name*> ``-lh.label`` and <*name*> ``-rh.label`` ,
respectively.
Individual label files can be loaded from Labels/Load label... . All label files in a directory can be
@@ -1879,8 +1879,8 @@ from w and stc files containing single time slice (static) and dynamic
data (movies), respectively. These data files can be produced by mne_make_movie ,
FreeSurfer software, and custom programs or Matlab scripts.
-The names of the files to be imported should end with ``-`` <hemi> .<type> , where <hemi> indicates
-the hemisphere (``lh`` or ``rh`` and <type> is ``w`` or ``stc`` .
+The names of the files to be imported should end with ``-`` <*hemi*> .<*type*> , where <*hemi*> indicates
+the hemisphere (``lh`` or ``rh`` and <*type*> is ``w`` or ``stc`` .
Overlays are managed from the dialog shown in :ref:`CACIGHEJ` which is invoked from File/Manage overlays... .
@@ -2331,7 +2331,7 @@ The saving and loading choices are:
**Save MRI set**
This option searches for a file called COR.fif in $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets.
- The file is copied to COR-<username>-<date>-<time>.fif
+ The file is copied to COR-<*username*>-<*date*>-<*time*>.fif
and the current MEG/MRI coordinate transformation as well as the
fiducial locations in MRI coordinates are inserted.
@@ -2389,21 +2389,21 @@ Suggested usage:
- Set the SUBJECTS_DIR correctly.
-- Run mkheadsurf: ``mkheadsurf -subjid`` <subject> .
+- Run mkheadsurf: ``mkheadsurf -subjid`` <*subject*> .
-- Goto the directory ``$SUBJECTS_DIR/`` <subject> ``/bem`` .
+- Goto the directory ``$SUBJECTS_DIR/`` <*subject*> ``/bem`` .
-- Convert the head surface file: ``mne_surf2bem --surf ../surf/lh.smseghead --id 4 --check --fif`` <subject> ``-head-dense.fif``
+- Convert the head surface file: ``mne_surf2bem --surf ../surf/lh.smseghead --id 4 --check --fif`` <*subject*> ``-head-dense.fif``
-- Rename the existing head surface file to <subject> ``-head-sparse.fif``
+- Rename the existing head surface file to <*subject*> ``-head-sparse.fif``
-- Copy <subject> ``-head-dense.fif`` to <subject> ``-head.fif``
+- Copy <*subject*> ``-head-dense.fif`` to <*subject*> ``-head.fif``
- Click Reload in the viewer
window.
After this you can switch between the dense and smooth head
-surface tessellations by copying either <subject> ``-head-dense.fif`` or <subject> ``-head-sparse.fif`` to <subject> ``-head.fif`` .
+surface tessellations by copying either <*subject*> ``-head-dense.fif`` or <*subject*> ``-head-sparse.fif`` to <*subject*> ``-head.fif`` .
If you have Matlab software available on your system, you
can also benefit from the script mne_make_scalp_surfaces .
@@ -2416,7 +2416,7 @@ and 'sparse' scalp surface tessellations. The
dense tessellation contains the output of mkheadsurf while
the medium and sparse tessellations comprise 30,000 and 2,500 triangles,
respectively. You can then make a symbolic link of one of these
-to <subject> ``-head.fif`` .
+to <*subject*> ``-head.fif`` .
The medium grade tessellation is an excellent compromize between
geometric accuracy and speed in the coordinate system alignment.
@@ -2438,7 +2438,7 @@ There a three supported ways to create this file:
function (not yet written) to create this file.
- Copy a MRI description file with the MEG-MRI coordinate transformation
- created with MRIlab (typically $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets/COR-<date>.fif
+ created with MRIlab (typically $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets/COR-<*date*>.fif
to $SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-fiducials.fif.
- For the average subject, fsaverage ,
diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst
index 31d1b50..4b4d04f 100755
--- a/doc/source/manual/browse.rst
+++ b/doc/source/manual/browse.rst
@@ -48,18 +48,18 @@ Common options
List the command-line options.
-**\---cd <dir>**
+**\---cd <*dir*>**
Change to this directory before starting.
-**\---raw <name>**
+**\---raw <*name*>**
Specifies the raw data file to be opened. This option is required
for batch version, mne_process_raw. If
a raw data file is not specified for the interactive version, mne_browse_raw ,
and empty interactive browser will open.
-**\---grad <number>**
+**\---grad <*number*>**
Apply software gradient compensation of the given order to the data loaded
with the ``--raw`` option. This option is effective only
@@ -74,18 +74,18 @@ Common options
For interactive data loading, the software gradient compensation
is specified in the corresponding file selection dialog, see :ref:`CACDCHAJ`.
-**\---filtersize <size>**
+**\---filtersize <*size*>**
Adjust the length of the FFT to be applied in filtering. The number will
- be rounded up to the next power of two. If the size is INLINE_EQUATION,
- the corresponding length of time is INLINE_EQUATION,
- where INLINE_EQUATION is the sampling frequency
+ be rounded up to the next power of two. If the size is :math:`N`,
+ the corresponding length of time is :math:`N/f_s`,
+ where :math:`f_s` is the sampling frequency
of your data. The filtering procedure includes overlapping tapers
- of length INLINE_EQUATION so that the total FFT
- length will actually be INLINE_EQUATION. This
+ of length :math:`N/2` so that the total FFT
+ length will actually be :math:`2N`. This
value cannot be changed after the program has been started.
-**\---highpass <value/Hz>**
+**\---highpass <*value/Hz*>**
Highpass filter frequency limit. If this is too low with respect
to the selected FFT length and, the data will not be highpass filtered. It
@@ -95,24 +95,24 @@ Common options
no highpass filter apart from that used during the acquisition will
be in effect.
-**\---highpassw <value/Hz>**
+**\---highpassw <*value/Hz*>**
The width of the transition band of the highpass filter. The default
- is 6 frequency bins, where one bin is INLINE_EQUATION. This
+ is 6 frequency bins, where one bin is :math:`f_s / (2N)`. This
value cannot be adjusted in the interactive version of the program.
-**\---lowpass <value/Hz>**
+**\---lowpass <*value/Hz*>**
Lowpass filter frequency limit. This value can be adjusted in the interactive
version of the program. The default is 40 Hz.
-**\---lowpassw <value/Hz>**
+**\---lowpassw <*value/Hz*>**
The width of the transition band of the lowpass filter. This value
can be adjusted in the interactive version of the program. The default
is 5 Hz.
-**\---eoghighpass <value/Hz>**
+**\---eoghighpass <*value/Hz*>**
Highpass filter frequency limit for EOG. If this is too low with respect
to the selected FFT length and, the data will not be highpass filtered.
@@ -122,19 +122,19 @@ Common options
no highpass filter apart from that used during the acquisition will
be in effect.
-**\---eoghighpassw <value/Hz>**
+**\---eoghighpassw <*value/Hz*>**
The width of the transition band of the EOG highpass filter. The default
- is 6 frequency bins, where one bin is INLINE_EQUATION.
+ is 6 frequency bins, where one bin is :math:`f_s / (2N)`.
This value cannot be adjusted in the interactive version of the
program.
-**\---eoglowpass <value/Hz>**
+**\---eoglowpass <*value/Hz*>**
Lowpass filter frequency limit for EOG. This value can be adjusted in
the interactive version of the program. The default is 40 Hz.
-**\---eoglowpassw <value/Hz>**
+**\---eoglowpassw <*value/Hz*>**
The width of the transition band of the EOG lowpass filter. This value
can be adjusted in the interactive version of the program. The default
@@ -145,13 +145,13 @@ Common options
Do not filter the data. This initial value can be changed in the
interactive version of the program.
-**\---digtrig <name>**
+**\---digtrig <*name*>**
Name of the composite digital trigger channel. The default value
is 'STI 014'. Underscores in the channel name
will be replaced by spaces.
-**\---digtrigmask <number>**
+**\---digtrigmask <*number*>**
Mask to be applied to the trigger channel values before considering them.
This option is useful if one wants to set some bits in a don't care
@@ -185,12 +185,12 @@ version only.
on. These kind of data should never be used for source localization
without further processing with Elekta-Neuromag software.
-**\---deriv <name>**
+**\---deriv <*name*>**
Specifies the name of a derivation file. This overrides the use
of a standard derivation file, see :ref:`CACFHAFH`.
-**\---sel <name>**
+**\---sel <*name*>**
Specifies the channel selection file to be used. This overrides
the use of the standard channel selection files, see :ref:`CACCJEJD`.
@@ -202,7 +202,7 @@ Batch-mode options
These options apply to the batch-mode version, mne_process_raw only.
-**\---proj <name>**
+**\---proj <*name*>**
Specify the name of the file of the file containing a signal-space
projection (SSP) operator. If ``--proj`` options are present
@@ -228,14 +228,14 @@ These options apply to the batch-mode version, mne_process_raw only.
eight options define the parameters of the noise subspace estimation. More
information on the signal-space projection can be found in :ref:`CACCHABI`.
-**\---projevent <no>**
+**\---projevent <*no*>**
Specifies the events which identify the time points of interest
for projector calculation. When this option is present, ``--projtmin`` and ``--projtmax`` are
relative to the time point of the event rather than the whole raw
data file.
-**\---projtmin <time/s>**
+**\---projtmin <*time/s*>**
Specify the beginning time for the calculation of the covariance matrix
which serves as the basis for the new SSP operator. This option
@@ -243,7 +243,7 @@ These options apply to the batch-mode version, mne_process_raw only.
of the raw data file otherwise. This option is effective only if ``--makeproj`` or ``--saveprojtag`` options
are present.
-**\---projtmax <time/s>**
+**\---projtmax <*time/s*>**
Specify the ending time for the calculation of the covariance matrix which
serves as the basis for the new SSP operator. This option is required
@@ -251,14 +251,14 @@ These options apply to the batch-mode version, mne_process_raw only.
file otherwise. This option is effective only if ``--makeproj`` or ``--saveprojtag`` options
are present.
-**\---projngrad <number>**
+**\---projngrad <*number*>**
Number of SSP components to include for planar gradiometers (default
= 5). This value is system dependent. For example, in a well-shielded
quiet environment, no planar gradiometer projections are usually
needed.
-**\---projnmag <number>**
+**\---projnmag <*number*>**
Number of SSP components to include for magnetometers / axial gradiometers
(default = 8). This value is system dependent. For example, in a
@@ -266,32 +266,32 @@ These options apply to the batch-mode version, mne_process_raw only.
while in a noisy environment with light shielding even more than
8 components may be necessary.
-**\---projgradrej <value/ fT/cm>**
+**\---projgradrej <*value/ fT/cm*>**
Rejection limit for planar gradiometers in the estimation of the covariance
matrix frfixom which the new SSP operator is derived. The default
value is 2000 fT/cm. Again, this value is system dependent.
-**\---projmagrej <value/ fT>**
+**\---projmagrej <*value/ fT*>**
Rejection limit for planar gradiometers in the estimation of the covariance
matrix from which the new SSP operator is derived. The default value
is 3000 fT. Again, this value is system dependent.
-**\---saveprojtag <tag>**
+**\---saveprojtag <*tag*>**
This option defines the names of files to hold the SSP operator.
If this option is present the ``--makeproj`` option is
implied. The SSP operator file name is formed by removing the trailing ``.fif`` or ``_raw.fif`` from
- the raw data file name by appending <tag> .fif
- to this stem. Recommended value for <tag> is ``-proj`` .
+ the raw data file name by appending <*tag*> .fif
+ to this stem. Recommended value for <*tag*> is ``-proj`` .
**\---saveprojaug**
Specify this option if you want to use the projection operator file output
in the Elekta-Neuromag Signal processor (graph) software.
-**\---eventsout <name>**
+**\---eventsout <*name*>**
List the digital trigger channel events to the specified file. By default,
only transitions from zero to a non-zero value are listed. If multiple
@@ -303,7 +303,7 @@ These options apply to the batch-mode version, mne_process_raw only.
List all transitions to file specified with the ``--eventsout`` option.
-**\---events <name>**
+**\---events <*name*>**
Specifies the name of a fif or text format event file (see :ref:`CACBCEGC`) to be associated with a raw data file to be
processed. If multiple raw data files are specified, the number
@@ -316,7 +316,7 @@ These options apply to the batch-mode version, mne_process_raw only.
if it ends with ``.fif`` , the file is assumed to be in
fif format, otherwise a text file is expected.
-**\---ave <name>**
+**\---ave <*name*>**
Specifies the name of an off-line averaging description file. For details
of the format of this file, please consult :ref:`CACBBDGC`.
@@ -326,21 +326,21 @@ These options apply to the batch-mode version, mne_process_raw only.
the raw data files in the order given. If it is smaller, the last
description file will be used for the remaining raw data files.
-**\---saveavetag <tag>**
+**\---saveavetag <*tag*>**
If this option is present and averaging is evoked with the ``--ave`` option,
the outfile and logfile options in the averaging description file
are ignored. Instead, trailing ``.fif`` or ``_raw.fif`` is
- removed from the raw data file name and <tag> ``.fif`` or <tag> ``.log`` is appended
+ removed from the raw data file name and <*tag*> ``.fif`` or <*tag*> ``.log`` is appended
to create the output and log file names, respectively.
-**\---gave <name>**
+**\---gave <*name*>**
If multiple raw data files are specified as input and averaging
is requested, the grand average over all data files will be saved
- to <name> .
+ to <*name*> .
-**\---cov <name>**
+**\---cov <*name*>**
Specify the name of a description file for covariance matrix estimation. For
details of the format of this file, please see :ref:`CACEBACG`.
@@ -350,13 +350,13 @@ These options apply to the batch-mode version, mne_process_raw only.
files in the order given. If it is smaller, the last description
file will be used for the remaining raw data files.
-**\---savecovtag <tag>**
+**\---savecovtag <*tag*>**
If this option is present and covariance matrix estimation is evoked with
the ``--cov`` option, the outfile and logfile options in
the covariance estimation description file are ignored. Instead,
trailing ``.fif`` or ``_raw.fif`` is removed from
- the raw data file name and <tag> .fif or <tag> .log
+ the raw data file name and <*tag*> .fif or <*tag*> .log
is appended to create the output and log file names, respectively.
For compatibility with other MNE software scripts, ``--savecovtag -cov`` is recommended.
@@ -368,26 +368,26 @@ These options apply to the batch-mode version, mne_process_raw only.
option the output files will be generated in the current working
directory instead.
-**\---gcov <name>**
+**\---gcov <*name*>**
If multiple raw data files are specified as input and covariance matrix estimation
is requested, the grand average over all data files will be saved
- to <name> . The details of
+ to <*name*> . The details of
the covariance matrix estimation are given in :ref:`CACHAAEG`.
-**\---save <name>**
+**\---save <*name*>**
Save a filtered and optionally down-sampled version of the data
- file to <name> . If multiple
+ file to <*name*> . If multiple
raw data files are specified, an equal number of ``--save`` options
- should be present. If <filename> ends
+ should be present. If <*filename*> ends
with ``.fif`` or ``_raw.fif`` , these endings are
deleted. After these modifications, ``_raw.fif`` is inserted
after the remaining part of the file name. If the file is split
into multiple parts (see ``--split`` option below), the
- additional parts will be called <name> ``-`` <number> ``_raw.fif``
+ additional parts will be called <*name*> ``-`` <*number*> ``_raw.fif``
-**\---split <size/MB>**
+**\---split <*size/MB*>**
Specifies the maximum size of the raw data files saved with the ``--save`` option.
By default, the output is split into files which are just below
@@ -398,7 +398,7 @@ These options apply to the batch-mode version, mne_process_raw only.
Do not include any subject information in the output files created with
the ``--save`` option.
-**\---decim <number>**
+**\---decim <*number*>**
The data are decimated by this factor before saving to the file
specified with the ``--save`` option. For decimation to
@@ -469,9 +469,9 @@ the data stored to disk.
When a raw data file is opened, the digital trigger channel
is scanned for events. For large files this may take a while.
-.. note:: After scanning the trigger channel for events, mne_browse_raw and mne_process_raw produce a fif file containing the event information. This file will be called <raw data file name without fif extension> ``-eve.fif`` . If the same raw data file is opened again, this file will be consulted for event information thus making it unnecessary to scan through the file for trigger line events.
+.. note:: After scanning the trigger channel for events, mne_browse_raw and mne_process_raw produce a fif file containing the event information. This file will be called <*raw data file name without fif extension*> ``-eve.fif`` . If the same raw data file is opened again, this file will be consulted for event information thus making it unnecessary to scan through the file for trigger line events.
-.. note:: You can produce the fif event file by running mne_process_raw as follows: ``mne_process_raw --raw`` <raw data file> . The fif format event files can be read and written with the mne_read_events and mne_write_events functions in the MNE Matlab toolbox, see :ref:`ch_matlab`.
+.. note:: You can produce the fif event file by running mne_process_raw as follows: ``mne_process_raw --raw`` <*raw data file*> . The fif format event files can be read and written with the mne_read_events and mne_write_events functions in the MNE Matlab toolbox, see :ref:`ch_matlab`.
.. _CACBHGFE:
@@ -504,11 +504,11 @@ three times the lowpass filter corner frequency. The output will
be split into files which are just below 2 GB so that the fif file
maximum size is not exceed.
-If <filename> ends
+If <*filename*> ends
with ``.fif`` or ``_raw.fif`` , these endings are
deleted. After these modifications, ``_raw.fif`` is inserted
after the remaining part of the file name. If the file is split
-into multiple parts, the additional parts will be called <name> ``-`` <number> ``_raw.fif`` .
+into multiple parts, the additional parts will be called <*name*> ``-`` <*number*> ``_raw.fif`` .
For downsampling and saving options in mne_process_raw ,
see :ref:`CACFAAAJ`.
@@ -693,7 +693,7 @@ The items in the dialog have the following functions:
**Lowpass transition (Hz)**
- The width of the INLINE_EQUATION-shaped transition
+ The width of the :math:`\cos^2`-shaped transition
from one to zero, centered at the Lowpass value.
**Filter active**
@@ -732,7 +732,7 @@ The items in the dialog have the following functions:
Sets the scale for MEG planar gradiometer channels in fT/cm. All scale
values are defined from zero to maximum, *i.e.*,
- the viewport where signals are plotted in have the limits ±<scale value> .
+ the viewport where signals are plotted in have the limits ± <*scale value*> .
**MEG axmult (cm)**
@@ -740,13 +740,13 @@ The items in the dialog have the following functions:
by multiplying the gradiometer scale by this number, yielding units
of fT.
-**EEG (INLINE_EQUATION)**
+**EEG (:math:`\mu`V)** EQUATION PROBLEM
- The scale for EEG channels in INLINE_EQUATION.
+ The scale for EEG channels in :math:`\mu`V. EQUATION PROBLEM
-**EOG (INLINE_EQUATION)**
+**EOG (:math:`\mu`V)** EQUATION PROBLEM
- The scale for EOG channels in INLINE_EQUATION.
+ The scale for EOG channels in :math:`\mu`V. EQUATION PROBLEM
**ECG (mV)**
@@ -1038,23 +1038,22 @@ returns to the default layout.
The format of the layout files is:
-<plot area limits> <viewport definition #1>
-...<viewport definition #N>
+ <*plot area limits*> <*viewport definition #1*>
+... <*viewport definition #N*>
-The <plot area limits> define
-the size of the plot area (INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION)
-which should accommodate all view ports. When the layout is used, the
+The <*plot area limits*> define
+the size of the plot area (:math:`x_{min}\ x_{max}\ y_{min}\ y_{max}`) which should accommodate all view ports. When the layout is used, the
plot area will preserve its aspect ratio; if the plot window has
a different aspect ratio, there will be empty space on the sides.
The viewports define the locations of the individual channels
in the plot. Each viewport definition consists of
-<number> INLINE_EQUATION INLINE_EQUATION <width> <height> < name> [:<name> ]...
+ <*number*> :math:`x_0\ y_0` <*width*> <*height*> <*name*> [: <*name*> ]...
-where number is a viewport number (not used by the MNE software), INLINE_EQUATION and INLINE_EQUATION are
-the coordinates of the lower-left corner of the viewport, <width> and <height> are
-the viewport dimensions, and <name> is
+where number is a viewport number (not used by the MNE software), :math:`x_0` and :math:`y_0` are
+the coordinates of the lower-left corner of the viewport, <*width*> and <*height*> are
+the viewport dimensions, and <*name*> is
a name of a channel. Multiple channel names can be specified by
separating them with a colon.
@@ -1138,11 +1137,11 @@ The items in the dialog have the following functions:
Rejection criterion for MEG magnetometers and axial gradiometers.
-**EEG rejection ( INLINE_EQUATIONV)**
+EEG rejection (:math:`\mu`V) EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
Rejection criterion for EEG channels.
-**EOG rejection ( INLINE_EQUATIONV)**
+**EOG rejection (:math:`\mu`V)** EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
Rejection criterion for EOG channels.
@@ -1161,11 +1160,11 @@ The items in the dialog have the following functions:
Signal detection criterion for MEG magnetometers and axial gradiometers.
-**EEG no signal ( INLINE_EQUATIONV)**
+**EEG no signal (:math:`\mu`V)** EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
Signal detection criterion for EEG channels.
-**EOG no signal ( INLINE_EQUATIONV)**
+**EOG no signal (:math:`\mu`V)** EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
Signal detection criterion for EOG channels.
@@ -1460,10 +1459,10 @@ mouse can be used to browse the data as follows:
**Left and right arrow keys**
If a single time point is selected (green line), move the time point forward
- and backward by INLINE_EQUATION. If the shift
- key is down, the time point is moved by INLINE_EQUATION.
+ and backward by :math:`\pm 1` ms. If the shift
+ key is down, the time point is moved by :math:`\pm 10` ms.
If the control key is down (with or without shift), the time point
- is moved by INLINE_EQUATION. If mne_browse_raw is
+ is moved by :math:`\pm 100` ms. If mne_browse_raw is
controlling mne_analyze (see :ref:`CACGHEGC`), the mne_analyze displays
will be updated accordingly. If the picked time point falls outside
the currently displayed section of data, the display will be automatically
@@ -1476,7 +1475,7 @@ mouse can be used to browse the data as follows:
**Rotate the trackball left/right or rotate the wheel with shift down**
Scroll backward or forward in the data by one screen. With Alt key (Command or Apple key
- in the Mac keyboard), the amount of scrolling will be INLINE_EQUATION instead
+ in the Mac keyboard), the amount of scrolling will be :math:`1` s instead
of the length of one screen. If shift key is held down with the
trackball, both left/right and up/down movements scroll the data
in time.
@@ -1509,7 +1508,7 @@ If a data files has annotations (user-defined events) associated
with it in mne_browse_raw , information
about them is automatically saved to an annotation file when a data file is closed, *i.e.*,
when you quit mne_browse_raw or
-load a new data file. This annotation file is called <raw data file name without fif extension> ``-annot.fif`` and
+load a new data file. This annotation file is called <*raw data file name without fif extension*> ``-annot.fif`` and
will be stored in the same directory as the raw data file. Therefore,
write permission to this directory is required to save the annotation
file.
@@ -1651,11 +1650,11 @@ on the digital trigger line in a raw data file. Any lines beginning
with the pound sign (``#`` ) are considered as comments.
The format of the event file data is:
-<sample> <time> <from> <to> <text>
+ <*sample*> <*time*> <*from*> <*to*> <*text*>
where
-**<sample>**
+** <*sample*>**
is
the sample number. This sample number takes into account the initial
@@ -1663,38 +1662,38 @@ where
and/or FIFF_DATA_SKIP tags in the beginning of raw data. Therefore,
the event file contents are independent of the Keep initial skip setting in the open dialog.
-**<time>**
+** <*time*>**
is
the time from the beginning of the file to this sample in seconds.
-**<from>**
+** <*from*>**
is
- the value of the digital trigger channel at <sample> -1.
+ the value of the digital trigger channel at <*sample*> -1.
-**<to>**
+** <*to*>**
is
- the value of the digital trigger channel at <sample> .
+ the value of the digital trigger channel at <*sample*> .
-**<text>**
+** <*text*>**
is
an optional annotation associated with the event. This comment will
be displayed in the event list and on the message line when you
move to an event.
-When an event file is read back, the <sample> value
-will be primarily used to specify the time. If you want the <time> to
+When an event file is read back, the <*sample*> value
+will be primarily used to specify the time. If you want the <*time*> to
be converted to the sample number instead, specify a negative value
-for <sample> .
+for <*sample*> .
Each event file starts with a "pseudo event" where
-both <from> and <to> fields
+both <*from*> and <*to*> fields
are equal to zero.
-.. warning:: In previous versions of the MNE software, the event files did not contain the initial empty pseudo event. In addition the sample numbers did not take into account the initial empty space in the raw data files. The present version of MNE software is still backwards compatible with the old version of the event files and interprets the sample numbers appropriately. However, the recognition of the old and new event file formats depends on the initial pseudo [...]
+.. warning:: In previous versions of the MNE software, the event files did not contain the initial empty pseudo event. In addition the sample numbers did not take into account the initial empty space in the raw data files. The present version of MNE software is still backwards compatible with the old version of the event files and interprets the sample numbers appropriately. However, the recognition of the old and new event file formats depends on the initial pseudo [...]
.. note:: If you have created Matlab, Excel or other scripts to process the event files, they may need revision to include the initial pseudo event in order for mne_browse_raw and mne_process_raw to recognize the edited event files correctly.
@@ -1832,12 +1831,12 @@ files.
The general format of the description file is:
``average {``
-<common parameters>
+ <*common parameters*>
``category {``
-<category definition parameters>
+ <*category definition parameters*>
``}``
-....``}``
+... ``}``
The file may contain arbitrarily many categories. The word ``category`` interchangeable
with ``condition`` .
@@ -1852,13 +1851,13 @@ Common parameters
The average definition starts with the common parameters.
They include:
-**outfile <name>**
+**outfile <*name*>**
The name of the file where the averages are to be stored. In interactive
mode, this can be omitted. The resulting average structure can be
viewed and stored from the Manage averages window.
-**eventfile <name>**
+**eventfile <*name*>**
Optional file to contain event specifications. If this file is present, the
trigger events in the raw data file are ignored and this file is
@@ -1867,44 +1866,44 @@ They include:
to be in fif format, otherwise a text file is expected. The text event
file format is described in :ref:`CACBCEGC`.
-**logfile <name>**
+**logfile <*name*>**
This optional file will contain detailed information about the averaging
process. In the interactive mode, the log information can be viewed
from the Manage averages window.
-**gradReject <value / T/m>**
+**gradReject <*value / T/m*>**
Rejection limit for MEG gradiometer channels. If the peak-to-peak amplitude
within the extracted epoch exceeds this value on any of the gradiometer
channels, the epoch will be omitted from the average.
-**magReject <value / T>**
+**magReject <*value / T*>**
Rejection limit for MEG magnetometer and axial gradiometer channels.
If the peak-to-peak amplitude within the extracted epoch exceeds
this value on any of the magnetometer or axial gradiometer channels,
the epoch will be omitted from the average.
-**eegReject <value / V>**
+**eegReject <*value / V*>**
Rejection limit for EEG channels. If the peak-to-peak amplitude within
the extracted epoch exceeds this value on any of the EEG channels,
the epoch will be omitted from the average.
-**eogReject <value / V>**
+**eogReject <*value / V*>**
Rejection limit for EOG channels. If the peak-to-peak amplitude within
the extracted epoch exceeds this value on any of the EOG channels,
the epoch will be omitted from the average.
-**ecgReject <value / V>**
+**ecgReject <*value / V*>**
Rejection limit for ECG channels. If the peak-to-peak amplitude within
the extracted epoch exceeds this value on any of the ECG channels,
the epoch will be omitted from the average.
-**gradFlat <value / T/m>**
+**gradFlat <*value / T/m*>**
Signal detection criterion for MEG planar gradiometers. The peak-to-peak
value of all planar gradiometer signals must exceed this value,
@@ -1912,24 +1911,24 @@ They include:
with saturated or otherwise dysfunctional channels. The default value
is zero, *i.e.*, no rejection.
-**magFlat <value / T>**
+**magFlat <*value / T*>**
Signal detection criterion for MEG magnetometers and axial gradiometers
channels.
-**eegFlat <value / V>**
+**eegFlat <*value / V*>**
Signal detection criterion for EEG channels.
-**eogFlat <value / V>**
+**eogFlat <*value / V*>**
Signal detection criterion for EOG channels.
-**ecgFlat <value / V>**
+**ecgFlat <*value / V*>**
Signal detection criterion for ECG channels.
-**stimIgnore <time / s>**
+**stimIgnore <*time / s*>**
Ignore this many seconds on both sides of the trigger when considering
the epoch. This parameter is useful for ignoring large stimulus artefacts, *e.g.*,
@@ -1942,14 +1941,14 @@ They include:
If this option is included in the off-line averaging description
file, the following procedure is used to counteract this: if there is
a transition from zero to a nonzero value on the digital trigger channel
- at sample INLINE_EQUATION, the following sample
+ at sample :math:`n`, the following sample
will be checked for a transition from this nonzero value to another
nonzero value. If such an event pair is found, the two events will
be jointly considered as a transition from zero to the second non-zero
value. With the fixSkew option, mne_browse_raw/mne_process_raw behaves
like the Elekta-Neuromag on-line averaging and Maxfilter (TM) software.
-**name <text>**
+**name <*text*>**
A descriptive name for this set of averages. If the name contains multiple
words, enclose it in quotation marks "like this".
@@ -1965,7 +1964,7 @@ Category definition
A category (condition) is defined by the parameters listed
in this section.
-**event <number>**
+**event <*number*>**
The zero time point of an epoch to be averaged is defined by a transition
from zero to this number on the digital trigger channel. The interpretation
@@ -1973,27 +1972,27 @@ in this section.
the ignore and mask keywords. If multiple event parameters are present
for a category, all specified events will be included in the average.
-**ignore <number>**
+**ignore <*number*>**
If this parameter is specified the selected bits on trigger channel
values can be mask (set to zero) out prior to checking for an existence of
an event. For example, to ignore the values of trigger input lines three
- and eight, specify ``ignore 132`` (INLINE_EQUATION).
+ and eight, specify ``ignore 132`` (:math:`2^2 + 2^7 = 132`).
-**mask <number>**
+**mask <*number*>**
Works similarly to ignore except that a mask specifies the trigger channel
bits to be included. For example, to look at trigger input lines
one to three only, ignoring others, specify ``mask 7`` (INLINE_EQUATION)
-**prevevent <number>**
+**prevevent <*number*>**
Specifies the event that is required to occur immediately before
the event(s) specified with event parameter(s)
in order for averaging to occur. Only one previous event number
can be specified.
-**prevignore <number>**
+**prevignore <*number*>**
Works like ignore but for the
events specified with prevevent .
@@ -2001,21 +2000,21 @@ in this section.
missing, the mask implied by ignore and mask is
applied to prevevent as well.
-**prevmask <number>**
+**prevmask <*number*>**
Works like mask but for the events
specified with prevevent . If prevignore and prevmask are
missing, the mask implied by ignore and mask is
applied to prevevent as well.
-**nextevent <number>**
+**nextevent <*number*>**
Specifies the event that is required to occur immediately after
the event(s) specified with event parameter(s)
in order for averaging to occur. Only one next event number can
be specified.
-**nextignore <number>**
+**nextignore <*number*>**
Works like ignore but for the
events specified with nextevent .
@@ -2023,14 +2022,14 @@ in this section.
missing, the mask implied by ignore and mask is
applied to nextevent as well.
-**nextmask <number>**
+**nextmask <*number*>**
Works like mask but for the events
specified with nextevent . If nextignore and nextmask are
missing, the mask implied by ignore and mask is
applied to nextevent as well.
-**delay <time / s>**
+**delay <*time / s*>**
Adds a delay to the time of the occurrence of an event. Therefore,
if this parameter is positive, the zero time point of the epoch
@@ -2038,33 +2037,33 @@ in this section.
the parameter is negative, the zero time point of the epoch will
be earlier than the event. By default, there will be no delay.
-**tmin <time / s>**
+**tmin <*time / s*>**
Beginning time point of the epoch.
-**tmax <time / s>**
+**tmax <*time / s*>**
End time point of the epoch.
-**bmin <time / s>**
+**bmin <*time / s*>**
Beginning time point of the baseline. If both ``bmin`` and ``bmax`` parameters
are present, the baseline defined by this time range is subtracted
from each epoch before they are added to the average.
-**basemin <time / s>**
+**basemin <*time / s*>**
Synonym for bmin.
-**bmax <time / s>**
+**bmax <*time / s*>**
End time point of the baseline.
-**basemax <time / s>**
+**basemax <*time / s*>**
Synonym for bmax.
-**name <text>**
+**name <*text*>**
A descriptive name for this category. If the name contains multiple words,
enclose it in quotation marks "like this". The
@@ -2107,12 +2106,12 @@ description files.
The general format of the description file is:
``cov {``
-<common parameters>
+ <*common parameters*>
``def {``
-<covariance definition parameters>
+ <*covariance definition parameters*>
``}``
-....``}``
+... ``}``
The file may contain arbitrarily many covariance definitions,
starting with ``def`` .
@@ -2127,12 +2126,12 @@ Common parameters
The average definition starts with the common parameters.
They include:
-**outfile <name>**
+**outfile <*name*>**
The name of the file where the covariance matrix is to be stores. This
parameter is mandatory.
-**eventfile <name>**
+**eventfile <*name*>**
Optional file to contain event specifications. This file can be
either in fif or text format (see :ref:`CACBCEGC`). The event
@@ -2142,44 +2141,44 @@ They include:
raw data file are ignored and this event file is consulted instead.
The event file format is described in :ref:`CACBCEGC`.
-**logfile <name>**
+**logfile <*name*>**
This optional file will contain detailed information about the averaging
process. In the interactive mode, the log information can be viewed
from the Manage averages window.
-**gradReject <value / T/m>**
+**gradReject <*value / T/m*>**
Rejection limit for MEG gradiometer channels. If the peak-to-peak amplitude
within the extracted epoch exceeds this value on any of the gradiometer
channels, the epoch will be omitted from the average.
-**magReject <value / T>**
+**magReject <*value / T*>**
Rejection limit for MEG magnetometer and axial gradiometer channels.
If the peak-to-peak amplitude within the extracted epoch exceeds
this value on any of the magnetometer or axial gradiometer channels,
the epoch will be omitted from the average.
-**eegReject <value / V>**
+**eegReject <*value / V*>**
Rejection limit for EEG channels. If the peak-to-peak amplitude within
the extracted epoch exceeds this value on any of the EEG channels,
the epoch will be omitted from the average.
-**eogReject <value / V>**
+**eogReject <*value / V*>**
Rejection limit for EOG channels. If the peak-to-peak amplitude within
the extracted epoch exceeds this value on any of the EOG channels,
the epoch will be omitted from the average.
-**ecgReject <value / V>**
+**ecgReject <*value / V*>**
Rejection limit for ECG channels. If the peak-to-peak amplitude within
the extracted epoch exceeds this value on any of the ECG channels,
the epoch will be omitted from the average.
-**gradFlat <value / T/m>**
+**gradFlat <*value / T/m*>**
Signal detection criterion for MEG planar gradiometers. The peak-to-peak
value of all planar gradiometer signals must exceed this value,
@@ -2187,24 +2186,24 @@ They include:
with saturated or otherwise dysfunctional channels. The default value
is zero, *i.e.*, no rejection.
-**magFlat <value / T>**
+**magFlat <*value / T*>**
Signal detection criterion for MEG magnetometers and axial gradiometers
channels.
-**eegFlat <value / V>**
+**eegFlat <*value / V*>**
Signal detection criterion for EEG channels.
-**eogFlat <value / V>**
+**eogFlat <*value / V*>**
Signal detection criterion for EOG channels.
-**ecgFlat <value / V>**
+**ecgFlat <*value / V*>**
Signal detection criterion for ECG channels.
-**stimIgnore <time / s>**
+**stimIgnore <*time / s*>**
Ignore this many seconds on both sides of the trigger when considering
the epoch. This parameter is useful for ignoring large stimulus artefacts, *e.g.*,
@@ -2217,7 +2216,7 @@ They include:
If this option is included in the off-line averaging description
file, the following procedure is used to counteract this: if there is
a transition from zero to a nonzero value on the digital trigger channel
- at sample INLINE_EQUATION, the following sample
+ at sample :math:`n`, the following sample
will be checked for a transition from this nonzero value to another
nonzero value. If such an event pair is found, the two events will
be jointly considered as a transition from zero to the second non-zero
@@ -2241,7 +2240,7 @@ Covariance definitions
The covariance definitions starting with def specify the
epochs to be included in the estimation of the covariance matrix.
-**event <number>**
+**event <*number*>**
The zero time point of an epoch to be averaged is defined by a transition
from zero to this number on the digital trigger channel. The interpretation
@@ -2251,20 +2250,20 @@ epochs to be included in the estimation of the covariance matrix.
parameter is missing or set to zero, the covariance matrix is computed
over a section of the raw data, defined by the ``tmin`` and ``tmax`` parameters.
-**ignore <number>**
+**ignore <*number*>**
If this parameter is specified the selected bits on trigger channel
values can be mask (set to zero) out prior to checking for an existence of
an event. For example, to ignore the values of trigger input lines three
- and eight, specify ``ignore 132`` (INLINE_EQUATION).
+ and eight, specify ``ignore 132`` (:math:`2^2 + 2^7 = 132`).
-**mask <number>**
+**mask <*number*>**
Works similarly to ignore except that a mask specifies the trigger channel
bits to be included. For example, to look at trigger input lines
one to three only, ignoring others, specify ``mask 7`` (INLINE_EQUATION)
-**delay <time / s>**
+**delay <*time / s*>**
Adds a delay to the time of the occurrence of an event. Therefore,
if this parameter is positive, the zero time point of the epoch
@@ -2273,19 +2272,19 @@ epochs to be included in the estimation of the covariance matrix.
be earlier than the time of the event. By default, there will be
no delay.
-**tmin <time / s>**
+**tmin <*time / s*>**
Beginning time point of the epoch. If the ``event`` parameter
is zero or missing, this defines the beginning point of the raw
data range to be included.
-**tmax <time / s>**
+**tmax <*time / s*>**
End time point of the epoch. If the ``event`` parameter
is zero or missing, this defines the end point of the raw data range
to be included.
-**bmin <time / s>**
+**bmin <*time / s*>**
It is possible to remove a baseline from the epochs before they
are included in the covariance matrix estimation. This parameter
@@ -2294,15 +2293,15 @@ epochs to be included in the estimation of the covariance matrix.
Setting of ``bmin`` and ``bmax`` is always recommended
for epoch-based covariance matrix estimation.
-**basemin <time / s>**
+**basemin <*time / s*>**
Synonym for bmin.
-**bmax <time / s>**
+**bmax <*time / s*>**
End time point of the baseline, see above.
-**basemax <time / s>**
+**basemax <*time / s*>**
Synonym for bmax.
@@ -2367,54 +2366,54 @@ noise sources. Furthermore, it is implicitly assumed that the linear
space spanned by the significant external noise patters has a low
dimension.
-Without loss of generality we can always decompose any INLINE_EQUATION-channel
-measurement INLINE_EQUATION into its signal and
+Without loss of generality we can always decompose any :math:`n`-channel
+measurement :math:`b(t)` into its signal and
noise components as
.. math:: b(t) = b_s(t) + b_n(t)
-Further, if we know that INLINE_EQUATION is
-well characterized by a few field patterns INLINE_EQUATION,
+Further, if we know that :math:`b_n(t)` is
+well characterized by a few field patterns :math:`b_1 \dotso b_m`,
we can express the disturbance as
.. math:: b_n(t) = Uc_n(t) + e(t)\ ,
-where the columns of INLINE_EQUATION constitute
-an orthonormal basis for INLINE_EQUATION, INLINE_EQUATION is
-an INLINE_EQUATION-component column vector, and
-the error term INLINE_EQUATION is small and does
-not exhibit any consistent spatial distributions over time, *i.e.*, INLINE_EQUATION.
-Subsequently, we will call the column space of INLINE_EQUATION the
+where the columns of :math:`U` constitute
+an orthonormal basis for :math:`b_1 \dotso b_m`, :math:`c_n(t)` is
+an :math:`m`-component column vector, and
+the error term :math:`e(t)` is small and does
+not exhibit any consistent spatial distributions over time, *i.e.*, :math:`C_e = E \{e e^T\} = I`.
+Subsequently, we will call the column space of :math:`U` the
noise subspace. The basic idea of SSP is that we can actually find
-a small basis set INLINE_EQUATION such that the
+a small basis set :math:`b_1 \dotso b_m` such that the
conditions described above are satisfied. We can now construct the
orthogonal complement operator
.. math:: P_{\perp} = I - UU^T
-and apply it to INLINE_EQUATION yielding
+and apply it to :math:`b(t)` yielding
.. math:: b(t) = P_{\perp}b_s(t)\ ,
-since INLINE_EQUATION. The projection operator INLINE_EQUATION is
+since :math:`P_{\perp}b_n(t) = P_{\perp}Uc_n(t) \approx 0`. The projection operator :math:`P_{\perp}` is
called the signal-space projection operator and generally provides
considerable rejection of noise, suppressing external disturbances
by a factor of 10 or more. The effectiveness of SSP depends on two
factors:
-- The basis set INLINE_EQUATION should
+- The basis set :math:`b_1 \dotso b_m` should
be able to characterize the disturbance field patterns completely
and
-- The angles between the noise subspace space spanned by INLINE_EQUATION and the
- signal vectors INLINE_EQUATION should be as close
- to INLINE_EQUATION as possible.
+- The angles between the noise subspace space spanned by :math:`b_1 \dotso b_m` and the
+ signal vectors :math:`b_s(t)` should be as close
+ to :math:`\pi / 2` as possible.
If the first requirement is not satisfied, some noise will
-leak through because INLINE_EQUATION. If the any
-of the brain signal vectors INLINE_EQUATION is
+leak through because :math:`P_{\perp}b_n(t) \neq 0`. If the any
+of the brain signal vectors :math:`b_s(t)` is
close to the noise subspace not only the noise but also the signal
-will be attenuated by the application of INLINE_EQUATION and,
+will be attenuated by the application of :math:`P_{\perp}` and,
consequently, there might by little gain in signal-to-noise ratio. :ref:`CACFGIEC` demonstrates the effect of SSP on the Vectorview
magnetometer data. After the elimination of a three-dimensional
noise subspace, the absolute value of the noise is dampened approximately
@@ -2434,7 +2433,7 @@ please consult the references listed in :ref:`CEGIEEBB`.
An example of the effect of SSP
- The covariance matrix INLINE_EQUATION of noise data on the 102 Vectorview magnetometers was computed (a) before and (b) after the application of SSP with three-dimensional noise subspace. The plotted quantity is INLINE_EQUATION. Note that the vertical scale in (b) is ten times smaller than in (a).
+ The covariance matrix :math:`C_n` of noise data on the 102 Vectorview magnetometers was computed (a) before and (b) after the application of SSP with three-dimensional noise subspace. The plotted quantity is :math:`\sqrt {|(C_n)_{jk}|}`. Note that the vertical scale in (b) is ten times smaller than in (a).
.. _BABFFCHF:
@@ -2442,7 +2441,7 @@ Estimation of the noise subspace
================================
As described above, application of SSP requires the estimation
-of the signal vectors INLINE_EQUATION constituting
+of the signal vectors :math:`b_1 \dotso b_m` constituting
the noise subspace. The most common approach, also implemented in mne_browse_raw is
to compute a covariance matrix of empty room data, compute its eigenvalue
decomposition, and employ the eigenvectors corresponding to the
@@ -2455,8 +2454,8 @@ EEG average electrode reference
In the computation of EEG-based source estimates, the MNE
software employs the average-electrode reference, which means that
-the average over all electrode signals INLINE_EQUATION is
-subtracted from each INLINE_EQUATION:
+the average over all electrode signals :math:`v_1 \dotso v_p` is
+subtracted from each :math:`v_j`:
.. math:: v_{j}' = v_j - \frac{1}{p} \sum_{k} v_k\ .
@@ -2482,8 +2481,8 @@ Continuous raw data
If a covariance matrix of a raw data is computed the data
are checked for artefacts in 200-sample pieces. Let us collect the
-accepted INLINE_EQUATION samples from all channels to
-the vectors INLINE_EQUATION. The estimate of the covariance
+accepted :math:`M` samples from all channels to
+the vectors :math:`s_j,\ j = 1, \dotsc ,M`. The estimate of the covariance
matrix is then computed as:
.. math:: \hat{C} = \frac{1}{M - 1} \sum_{j = 1}^M {(s_j - \bar{s})(s_j - \bar{s})}^T
@@ -2518,10 +2517,10 @@ Let the vectors
.. math:: s_{rpj}\ ;\ p = 1 \dotsc P_r\ ;\ j = 1 \dotsc N_r\ ;\ r = 1 \dotsc R
be the samples from all channels in the baseline corrected epochs
-used to calculate the covariance matrix. In the above, INLINE_EQUATION is
-the number of accepted epochs in category INLINE_EQUATION, INLINE_EQUATION is
-the number of samples in the epochs of category INLINE_EQUATION,
-and INLINE_EQUATION is the number of categories.
+used to calculate the covariance matrix. In the above, :math:`P_r` is
+the number of accepted epochs in category :math:`r`, :math:`N_r` is
+the number of samples in the epochs of category :math:`r`,
+and :math:`R` is the number of categories.
If the recommended ``--keepsamplemean`` option
is specified in the covariance matrix definition file, the baseline
@@ -2548,8 +2547,8 @@ and
.. math:: N_C = \sum_{r = 1}^R {N_r (P_r - 1)}\ ,
-which reflects the fact that INLINE_EQUATION means
-are computed for category INLINE_EQUATION. It
+which reflects the fact that :math:`N_r` means
+are computed for category :math:`r`. It
is easy to see that the expression for the covariance matrix estimate
can be cast into a more convenient form
@@ -2563,8 +2562,8 @@ Combination of covariance matrix estimates
==========================================
Let us assume that we have computed multiple covariance matrix
-estimates INLINE_EQUATION with corresponding degrees
-of freedom INLINE_EQUATION. We can combine these
+estimates :math:`\hat{C_1} \dotso \hat{C_Q}` with corresponding degrees
+of freedom :math:`N_1 \dotso N_Q`. We can combine these
matrices together as
.. math:: C = \sum_q {\alpha_q \hat{C}_q}\ ,
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
index 95f0cc5..b5ab5c8 100755
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -87,17 +87,17 @@ The command-line options of mne_ctf2fiff are:
Produce a verbose listing of the conversion process to stdout.
-**\---ds <directory>**
+**\---ds <*directory*>**
Read the data from this directory
-**\---omit <filename>**
+**\---omit <*filename*>**
Read the names of channels to be omitted from this text file. Enter one
channel name per line. The names should match exactly with those
listed in the CTF data structures. By default, all channels are included.
-**\---fif <filename>**
+**\---fif <*filename*>**
The name of the output file. If the length of the raw data exceeds
the 2-GByte fif file limit, several output files will be produced.
@@ -118,37 +118,37 @@ The command-line options of mne_ctf2fiff are:
During conversion, the following files are consulted from
the ds directory:
-**<name> .res4**
+** <*name*> .res4**
This file contains most of the header information pertaining the acquisition.
-**<name> .hc**
+** <*name*> .hc**
This file contains the HPI coil locations in sensor and head coordinates.
-**<name> .meg4**
+** <*name*> .meg4**
This file contains the actual MEG data. If the data are split across several
files due to the 2-GByte file size restriction, the 'extension' files
- are called <name> ``.`` <number> ``_meg4`` .
+ are called <*name*> ``.`` <*number*> ``_meg4`` .
-**<name> .eeg**
+** <*name*> .eeg**
This is an optional input file containing the EEG electrode locations. More
details are given below.
-If the <name> ``.eeg`` file,
+If the <*name*> ``.eeg`` file,
produced from the Polhemus data file with CTF software, is present,
it is assumed to contain lines with the format:
-<number> <name> <x/cm> <y/cm> <z/cm>
+ <*number*> <*name*> <*x/cm*> <*y/cm*> <*z/cm*>
-The field <number> is
+The field <*number*> is
a sequential number to be assigned to the converted data point in
-the fif file. <name> is either
+the fif file. <*name*> is either
a name of an EEG channel, one of ``left`` , ``right`` ,
or ``nasion`` to indicate a fiducial landmark, or any word
-which is not a name of any channel in the data. If <name> is
+which is not a name of any channel in the data. If <*name*> is
a name of an EEG channel available in the data, the location is
included in the Polhemus data as an EEG electrode locations and
inserted as the location of the EEG electrode. If the name is one
@@ -202,7 +202,7 @@ The command-line options for mne_ctf_dig2fiff are:
List the command-line options.
-**\---dig <name>**
+**\---dig <*name*>**
Specifies the input data file in CTF output format.
@@ -210,12 +210,12 @@ The command-line options for mne_ctf_dig2fiff are:
Fiducial locations are numbered instead of labeled, see above.
-**\---hpts <name>**
+**\---hpts <*name*>**
Specifies the output hpts file. The format of this text file is
described in :ref:`CJADJEBH`.
-**\---fif <name>**
+**\---fif <*name*>**
Specifies the output fif file.
@@ -292,15 +292,15 @@ which has the following command-line options:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies the input data file.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output data file.
-**\---grad <number>**
+**\---grad <*number*>**
Specifies the desired compensation grade in the output file. The value
can be 1, 2, 3, or 101. The values starting from 101 will be used
@@ -330,16 +330,16 @@ This utility has the following command-line options:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies the input fif file containing the helmet sensor data.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output fif file which will contain both the helmet
sensor data and the compensation channel data.
-**\---ref <name>**
+**\---ref <*name*>**
Specifies a text file containing the reference sensor data.
@@ -398,30 +398,30 @@ The command line options of mne_create_comp_data are:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies the input text file containing the compensation data.
-**\---kind <value>**
+**\---kind <*value*>**
The compensation type to be stored in the output file with the data. This
value defaults to 101 for the Magnes compensation and does not need
to be changed.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output fif file containing the compensation channel weight
matrix INLINE_EQUATION, see :ref:`BEHDDFBI`.
The format of the text-format compensation data file is:
-<number of MEG helmet channels> <number of compensation channels included>
-<INLINE_EQUATION> <INLINE_EQUATION>INLINE_EQUATION
-<INLINE_EQUATION> <weights>
-<INLINE_EQUATION> <weights> INLINE_EQUATION
+ <*number of MEG helmet channels*> <*number of compensation channels included*>
+ <*INLINE_EQUATION*> <*INLINE_EQUATION*>INLINE_EQUATION
+ <*INLINE_EQUATION*> <*weights*>
+ <*INLINE_EQUATION*> <*weights*> INLINE_EQUATION
-In the above <INLINE_EQUATION> denote
-names of MEG helmet channels and <INLINE_EQUATION>
+In the above <*INLINE_EQUATION*> denote
+names of MEG helmet channels and <*INLINE_EQUATION*>
those of the compensation channels, respectively. If the channel
names contain spaces, they must be surrounded by quotes, for example, ``"MEG 0111"`` .
@@ -505,55 +505,55 @@ the following command-line options:
List the command-line options.
-**\---elp <filename>**
+**\---elp <*filename*>**
The name of the file containing the locations of the fiducials and
the HPI coils. This option is mandatory.
-**\---hsp <filename>**
+**\---hsp <*filename*>**
The name of the file containing the locations of the fiducials and additional
points on the head surface. This file is optional.
-**\---sns <filename>**
+**\---sns <*filename*>**
The name of file containing the sensor locations and orientations. This
option is mandatory.
-**\---hpi <filename>**
+**\---hpi <*filename*>**
The name of a text file containing the locations of the HPI coils
in the MEG device coordinate frame, given in millimeters. The order of
the coils in this file does not have to be the same as that in the elp file.
This option is mandatory.
-**\---raw <filename>**
+**\---raw <*filename*>**
Specifies the name of the raw data file. If this file is not specified, the
output fif file will only contain the measurement info block.
-**\---sfreq <value/Hz>**
+**\---sfreq <*value/Hz*>**
The sampling frequency of the data. If this option is not specified, the
sampling frequency defaults to 1000 Hz.
-**\---lowpass <value/Hz>**
+**\---lowpass <*value/Hz*>**
The lowpass filter corner frequency used in the data acquisition.
If not specified, this value defaults to 200 Hz.
-**\---highpass <value/Hz>**
+**\---highpass <*value/Hz*>**
The highpass filter corner frequency used in the data acquisition.
If not specified, this value defaults to 0 Hz (DC recording).
-**\---out <filename>**
+**\---out <*filename*>**
Specifies the name of the output fif format data file. If this file
is not specified, no output is produced but the elp , hpi ,
and hsp files are processed normally.
-**\---stim <chs>**
+**\---stim <*chs*>**
Specifies a colon-separated list of numbers of channels to be used
to synthesize a digital trigger channel. These numbers refer to
@@ -562,12 +562,12 @@ the following command-line options:
channel in the file. If this option is absent, the output file will
not contain a trigger channel.
-**\---stimthresh <value>**
+**\---stimthresh <*value*>**
The threshold value used when synthesizing the digital trigger channel,
see above. Defaults to 1.0.
-**\---add <chs>**
+**\---add <*chs*>**
Specifies a colon-separated list of numbers of channels to include between
the 157 default MEG channels and the digital trigger channel. These
@@ -643,11 +643,11 @@ The command-line options of mne_edf2fiff are:
List the command-line options.
-**\---edf <filename>**
+**\---edf <*filename*>**
Specifies the name of the raw data file to process.
-**\---tal <filename>**
+**\---tal <*filename*>**
List the time-stamped annotation list (TAL) data from an EDF+ file here.
This output is useful to assist in creating the annotation map file,
@@ -659,7 +659,7 @@ The command-line options of mne_edf2fiff are:
the absense of the ``--annotmap`` option default trigger number 1024
is used.
-**\---annotmap <filename>**
+**\---annotmap <*filename*>**
Specify a file which maps the labels of the TALs to numbers on a trigger
channel (STI 014) which will be added to the output file if this
@@ -670,7 +670,7 @@ The command-line options of mne_edf2fiff are:
annotation labeled with the text 'Trigger-1' will
be translated to the number 9 on the trigger channel.
-**\---elp <filename>**
+**\---elp <*filename*>**
Specifies the name of the an electrode location file. This file
is in the "probe" file format used by the *Source
@@ -684,7 +684,7 @@ The command-line options of mne_edf2fiff are:
When this option is encountered on the command line any previously
specified hpts file will be ignored.
-**\---hpts <filename>**
+**\---hpts <*filename*>**
Specifies the name of an electrode position file in the hpts format discussed
in :ref:`CJADJEBH`. The mandatory entries are the fiducial marker
@@ -699,7 +699,7 @@ The command-line options of mne_edf2fiff are:
Assumes that the digitization data in an hpts file
is given in meters instead of millimeters.
-**\---fif <filename>**
+**\---fif <*filename*>**
Specifies the name of the fif file to be output.
@@ -764,16 +764,16 @@ the following command-line options:
List the command-line options.
-**\---raw <filename>**
+**\---raw <*filename*>**
Specifies the name of the raw data file to process.
-**\---cal <filename>**
+**\---cal <*filename*>**
The name of the calibration data file. If calibration data are missing, the
calibration coefficients will be set to unity.
-**\---elp <filename>**
+**\---elp <*filename*>**
The name of the electrode location file. If this file is missing,
the electrode locations will be unspecified. This file is in the "probe" file
@@ -813,7 +813,7 @@ The command-line options of mne_brain_vision2fiff are:
List the command-line options.
-**\---header <name>**
+**\---header <*name*>**
The name of the BrainVision header file. The extension of this file
is ``vhdr`` . The header file typically refers to a marker
@@ -822,7 +822,7 @@ The command-line options of mne_brain_vision2fiff are:
The ``vmrk`` file is ignored if the ``--eximia`` option
is present.
-**\---dig <name>**
+**\---dig <*name*>**
The name of the fif file containing the digitization data.
@@ -841,19 +841,19 @@ The command-line options of mne_brain_vision2fiff are:
by the mne_eximia2fiff script,
see :ref:`BEHGCEHH`.
-**\---split <size/MB>**
+**\---split <*size/MB*>**
- Split the output data into several files which are no more than <size> MB.
+ Split the output data into several files which are no more than <*size*> MB.
By default, the output is split into files which are just below
2 GB so that the fif file maximum size is not exceeded.
-**\---out <filename>**
+**\---out <*filename*>**
- Specifies the name of the output fif format data file. If <filename> ends
+ Specifies the name of the output fif format data file. If <*filename*> ends
with ``.fif`` or ``_raw.fif`` , these endings are
deleted. After these modifications, ``_raw.fif`` is inserted
after the remaining part of the file name. If the file is split
- into multiple parts, the additional parts will be called <name> ``-`` <number> ``_raw.fif`` .
+ into multiple parts, the additional parts will be called <*name*> ``-`` <*number*> ``_raw.fif`` .
.. _BEHGCEHH:
@@ -925,23 +925,23 @@ The command-line options of mne_convert_dig_data are:
List the command-line options.
-**\---fif <name>**
+**\---fif <*name*>**
Specifies the name of an input fif file.
-**\---hpts <name>**
+**\---hpts <*name*>**
Specifies the name of an input hpts file.
-**\---elp <name>**
+**\---elp <*name*>**
Specifies the name of an input elp file.
-**\---fifout <name>**
+**\---fifout <*name*>**
Specifies the name of an output fif file.
-**\---hptsout <name>**
+**\---hptsout <*name*>**
Specifies the name of an output hpts file.
@@ -968,11 +968,11 @@ The hpts format digitzer
data file may contain comment lines starting with the pound sign
(#) and data lines of the form:
-<category> <identifier> <x/mm> <y/mm> <z/mm>
+ <*category*> <*identifier*> <*x/mm*> <*y/mm*> <*z/mm*>
where
-**<category>**
+** <*category*>**
defines the type of points. Allowed categories are: hpi , cardinal (fiducial ),eeg ,
and extra corresponding to head-position
@@ -981,7 +981,7 @@ where
recognize the fiducial as an
alias for cardinal .
-**<identifier>**
+** <*identifier*>**
identifies the point. The identifiers are usually sequential numbers. For
cardinal landmarks, 1 = left auricular point, 2 = nasion, and 3
@@ -989,7 +989,7 @@ where
the reference electrode. Some programs (not tkmedit )
accept electrode labels as identifiers in the eeg category.
-**<x/mm> , <y/mm> , <z/mm>**
+** <*x/mm*> , <*y/mm*> , <*z/mm*>**
Location of the point, usually in the MEG head coordinate system, see :ref:`BJEBIBAI`.
Some programs have options to accept coordinates in meters instead
@@ -1030,31 +1030,31 @@ the following command-line options:
List the command-line options.
-**\---src <filename>**
+**\---src <*filename*>**
The name of the volumetric source space file created with mne_volume_source_space .
The source space must have been created with the ``--mri`` option,
which adds the appropriate sparse trilinear interpolator matrix
to the source space.
-**\---w <filename>**
+**\---w <*filename*>**
The name of a w file to convert
into an MRI overlay.
-**\---stc <filename>**
+**\---stc <*filename*>**
The name of the stc file to convert
into an MRI overlay. If this file has many time frames, the output
file may be huge. Note: If both ``-w`` and ``--stc`` are
specified, ``-w`` takes precedence.
-**\---scale <number>**
+**\---scale <*number*>**
Multiply the stc or w by
this scaling constant before producing the overlay.
-**\---out <filename>**
+**\---out <*filename*>**
Specifies the name of the output MRI overlay file. The name must end
with either ``.mgh`` or ``.mgz`` identifying the
@@ -1079,13 +1079,13 @@ The command-line options are:
List the command-line options.
-**\---src <name>**
+**\---src <*name*>**
The source space to be listed. This can be either the output from mne_make_source_space
(*src.fif), output from the forward calculation (*fwd.fif), or
the output from the inverse operator decomposition (*inv.fif).
-**\---mri <name>**
+**\---mri <*name*>**
A file containing the transformation between the head and MRI coordinates
is specified with this option. This file can be either a Neuromag
@@ -1094,32 +1094,32 @@ The command-line options are:
If this file is included, the output will be in head coordinates.
Otherwise the source space will be listed in MRI coordinates.
-**\---dip <name>**
+**\---dip <*name*>**
Specifies the 'stem' for the Neuromag text format
- dipole files to be output. Two files will be produced: <stem> -lh.dip
- and <stem> -rh.dip. These correspond
+ dipole files to be output. Two files will be produced: <*stem*> -lh.dip
+ and <*stem*> -rh.dip. These correspond
to the left and right hemisphere part of the source space, respectively.
This source space data can be imported to MRIlab through the File/Import/Dipoles menu
item.
-**\---pnt <name>**
+**\---pnt <*name*>**
Specifies the 'stem' for Neuromag text format
- point files to be output. Two files will be produced: <stem> -lh.pnt
- and <stem> -rh.pnt. These correspond
+ point files to be output. Two files will be produced: <*stem*> -lh.pnt
+ and <*stem*> -rh.pnt. These correspond
to the left and right hemisphere part of the source space, respectively.
This source space data can be imported to MRIlab through the File/Import/Strings menu
item.
-**\---exclude <name>**
+**\---exclude <*name*>**
Exclude the source space points defined by the given FreeSurfer 'label' file
from the output. The name of the file should end with ``-lh.label``
if it refers to the left hemisphere and with ``-rh.label`` if
it lists points in the right hemisphere, respectively.
-**\---include <name>**
+**\---include <*name*>**
Include only the source space points defined by the given FreeSurfer 'label' file
to the output. The file naming convention is the same as described
@@ -1152,15 +1152,15 @@ The command-line options are:
List the command-line options.
-**\---bem <name>**
+**\---bem <*name*>**
The BEM file to be listed. The file name normally ends with -bem.fif or -bem-sol.fif .
-**\---out <name>**
+**\---out <*name*>**
The output file name.
-**\---id <number>**
+**\---id <*number*>**
Identify the surface to be listed. The surfaces are numbered starting with
the innermost surface. Thus, for a three-layer model the surface numbers
@@ -1211,12 +1211,12 @@ the following command-line options:
List the command-line options.
-**\---fif <name>**
+**\---fif <*name*>**
Specifies a fif format input file. The first surface (source space)
from this file will be read.
-**\---tri <name>**
+**\---tri <*name*>**
Specifies a text format input file. The format of this file is described in :ref:`BEHDEFCD`.
@@ -1238,17 +1238,17 @@ the following command-line options:
This option does not have any effect on the interpretation of the FreeSurfer surface
files specified with the ``--surf`` option.
-**\---surf <name>**
+**\---surf <*name*>**
Specifies a FreeSurfer format
input file.
-**\---dfs <name>**
+**\---dfs <*name*>**
Specifies the name of a dfs file to be converted. The surfaces produced
by BrainSuite are in the dfs format.
-**\---mghmri <name>**
+**\---mghmri <*name*>**
Specifies a mgh/mgz format MRI data file which will be used to define
the coordinate transformation to be applied to the data read from
@@ -1266,14 +1266,14 @@ the following command-line options:
Replaces existing volume geometry information. Used in conjunction
with the ``--mghmri`` option described above.
-**\---fifmri <name>**
+**\---fifmri <*name*>**
Specifies a fif format MRI destription file which will be used to define
the coordinate transformation to be applied to the data read from
a dfs file to bring it to the same coordinate system as the MRI stack
in the file.
-**\---trans <name>**
+**\---trans <*name*>**
Specifies the name of a text file which contains the coordinate
transformation to be applied to the data read from the dfs file
@@ -1290,25 +1290,25 @@ the following command-line options:
(LAS) with its origin in the right-posterior-inferior (RPI) corner
of the MRI stack.
-**\---shift <value/mm>**
+**\---shift <*value/mm*>**
Shift the surface vertices to the direction of the surface normals
by this amount before saving the surface.
-**\---surfout <name>**
+**\---surfout <*name*>**
Specifies a FreeSurfer format output file.
-**\---fifout <name>**
+**\---fifout <*name*>**
Specifies a fif format output file.
-**\---triout <name>**
+**\---triout <*name*>**
Specifies an ASCII output file that will contain the surface data
in the triangle file format desribed in :ref:`BEHDEFCD`.
-**\---pntout <name>**
+**\---pntout <*name*>**
Specifies a ASCII output file which will contain the vertex numbers only.
@@ -1322,7 +1322,7 @@ the following command-line options:
Defines the vertex ordering of ASCII triangle files to be output.
For details, see ``--swap`` option, above.
-**\---smfout <name>**
+**\---smfout <*name*>**
Specifies a smf (Simple Model Format) output file. For details of this
format, see http://people.scs.fsu.edu/~burkardt/data/smf.txt.
@@ -1363,7 +1363,7 @@ data as input. The command-line options are:
List the command-line options.
-**\---dir <directory>**
+**\---dir <*directory*>**
Specifies a directory containing the MRI volume in COR format. Any
previous ``--mgh`` options are cancelled when this option
@@ -1374,7 +1374,7 @@ data as input. The command-line options are:
Include the pixel data to the output file. This option is implied
with the ``--mgh`` option.
-**\---mgh <name>**
+**\---mgh <*name*>**
An MRI volume volume file in mgh or mgz format.
The ``--withdata`` option is implied with this type of
@@ -1385,12 +1385,12 @@ data as input. The command-line options are:
added to the output file. For definition of the coordinate transformations,
see :ref:`CHDEDFIB`.
-**\---talairach <name>**
+**\---talairach <*name*>**
Take the Talairach transform from this file instead of the one specified
in mgh/mgz files.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output file, which is a fif-format MRI description
file.
@@ -1417,13 +1417,13 @@ The command-line options are:
List the command-line options.
-**\---meas <name>**
+**\---meas <*name*>**
Specifies a measurement data file which provides INLINE_EQUATION.
A forward solution or an inverse operator file can also be specified
as implied by Table 5.1.
-**\---mri <name>**
+**\---mri <*name*>**
Specifies an MRI description or a standalone coordinate transformation
file produced by mne_analyze which
@@ -1432,7 +1432,7 @@ The command-line options are:
tries to find INLINE_EQUATION, INLINE_EQUATION, INLINE_EQUATION,
and INLINE_EQUATION from this file.
-**\---mgh <name>**
+**\---mgh <*name*>**
An MRI volume volume file in mgh or mgz format.
This file provides INLINE_EQUATION. The transformation INLINE_EQUATION will
@@ -1440,7 +1440,7 @@ The command-line options are:
The fixed transforms INLINE_EQUATION and INLINE_EQUATIONwill
be also created.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output file. If this option is not present, the collected transformations
will be output on screen but not saved.
@@ -1465,11 +1465,11 @@ The command-line options are:
List the command-line options.
-**\---ncov <name>**
+**\---ncov <*name*>**
The ncov file to be converted.
-**\---meas <name>**
+**\---meas <*name*>**
A fif format measurement file used to assign channel names to the noise-covariance
matrix elements. This file should have precisely the same channel
@@ -1495,24 +1495,24 @@ The command-line options are:
List the command-line options.
-**\---lspcov <name>**
+**\---lspcov <*name*>**
The LISP noise-covariance matrix file to be converted.
-**\---meas <name>**
+**\---meas <*name*>**
A fif format measurement file used to assign channel names to the noise-covariance
matrix elements. This file should have precisely the same channel
order within MEG and EEG as the LISP-format covariance matrix file.
-**\---out <name>**
+**\---out <*name*>**
The name of a fif format output file. The file name should end with
-cov.fif.text format output file. No information about the channel names
is included. The covariance matrix file is listed row by row. This
file can be loaded to MATLAB, for example
-**\---outasc <name>**
+**\---outasc <*name*>**
The name of a text format output file. No information about the channel
names is included. The covariance matrix file is listed row by row.
@@ -1549,7 +1549,7 @@ by mne_convert_mne_data are:
List the command-line options.
-**\---fwd <name>**
+**\---fwd <*name*>**
Specity the name of the forward solution file to be converted. Channels
specified with the ``--bad`` option will be excluded from
@@ -1577,19 +1577,19 @@ by mne_convert_mne_data are:
When creating a 'measurement' fif file, do not
output a forward model file, just the noise-covariance matrix.
-**\---senscov <name>**
+**\---senscov <*name*>**
Specifies the fif file containing a sensor covariance matrix to
be included with the output. If no other input files are specified
only the covariance matrix is output
-**\---srccov <name>**
+**\---srccov <*name*>**
Specifies the fif file containing the source covariance matrix to
be included with the output. Only diagonal source covariance files
can be handled at the moment.
-**\---bad <name>**
+**\---bad <*name*>**
Specifies the name of the file containing the names of the channels to
be omitted, one channel name per line. This does not affect the output
@@ -1599,8 +1599,8 @@ by mne_convert_mne_data are:
**\---fif**
Output the forward model and the noise-covariance matrix into 'measurement' fif
- files. The forward model files are tagged with <modalities> ``-meas-fwd.fif`` and
- the noise-covariance matrix files with <modalities> ``-meas-cov.fif`` .
+ files. The forward model files are tagged with <*modalities*> ``-meas-fwd.fif`` and
+ the noise-covariance matrix files with <*modalities*> ``-meas-cov.fif`` .
Here, modalities is ``-meg`` if MEG is included, ``-eeg`` if
EEG is included, and ``-meg-eeg`` if both types of signals
are present. The inclusion of modalities is controlled by the ``--meg`` and ``--eeg`` options.
@@ -1608,17 +1608,17 @@ by mne_convert_mne_data are:
**\---mat**
Output the data into MATLAB mat files. This is the default. The
- forward model files are tagged with <modalities> ``-fwd.mat`` forward model
+ forward model files are tagged with <*modalities*> ``-fwd.mat`` forward model
and noise-covariance matrix output, with ``-inv.mat`` for inverse
operator output, and with ``-inv-meas.mat`` for combined inverse
operator and measurement data output, respectively. The meaning
- of <modalities> is the same
+ of <*modalities*> is the same
as in the fif output, described above.
-**\---tag <name>**
+**\---tag <*name*>**
By default, all variables in the matlab output files start with
- MNE_. This option allows to change this prefix to <name> _.
+ MNE_. This option allows to change this prefix to <*name*> _.
**\---meg**
@@ -1630,7 +1630,7 @@ by mne_convert_mne_data are:
Include EEG channels from the forward solution and noise-covariance
matrix.
-**\---inv <name>**
+**\---inv <*name*>**
Output the inverse operator data from the specified file into a
mat file. The source and noise covariance matrices as well as active channels
@@ -1639,7 +1639,7 @@ by mne_convert_mne_data are:
the options ``--meg`` , ``--eeg`` , ``--senscov`` , ``--srccov`` , ``--noiseonly`` ,
and ``--bad`` do not affect the output of the inverse operator.
-**\---meas <name>**
+**\---meas <*name*>**
Specifies the file containing measurement data to be output together with
the inverse operator. The channels corresponding to the inverse operator
@@ -1647,16 +1647,16 @@ by mne_convert_mne_data are:
option is present. Otherwise, the channel selection given with ``--sel`` option will
be taken into account.
-**\---set <number>**
+**\---set <*number*>**
Select the data set to be output from the measurement file.
-**\---bmin <value/ms>**
+**\---bmin <*value/ms*>**
Specifies the baseline minimum value setting for the measurement signal
output.
-**\---bmax <value/ms>**
+**\---bmax <*value/ms*>**
Specifies the baseline maximum value setting for the measurement signal
output.
@@ -1676,16 +1676,16 @@ of options appropriate for your needs.
============================================ ======== ===================================================================================== ===============================
Desired output Format Required options Optional options
============================================ ======== ===================================================================================== ===============================
- forward model fif --fwd <name> --out <name> --meg and/or --eeg --fif --bad <name> --surfsrc
- forward model mat --fwd <name> --out <name> --meg and/or --eeg --bad <name> --surfsrc
- forward model and sensor covariance mat --fwd <name> --out <name> --senscov <name> --meg and/or --eeg --bad <name> --surfsrc
- sensor covariance fif --fwd <name> --out <name> --senscov <name> --noiseonly --fif --meg and/or --eeg --bad <name>
- sensor covariance mat --senscov <name> --out <name --bad <name>
- sensor covariance eigenvalues text --senscov <name> --out <name --eig --bad <name>
- evoked MEG/EEG data mat --meas <name> --out <name --sel <name> --set <number>
- evoked MEG/EEG data forward model mat --meas <name> --fwd <name> --out <name> --bad <name> --set <number>
- inverse operator data mat --inv <name> --out <name
- inverse operator data evoked MEG/EEG data mat --inv <name> --meas <name> --out <name
+ forward model fif --fwd <*name*> --out <*name*> --meg and/or --eeg --fif --bad <*name*> --surfsrc
+ forward model mat --fwd <*name*> --out <*name*> --meg and/or --eeg --bad <*name*> --surfsrc
+ forward model and sensor covariance mat --fwd <*name*> --out <*name*> --senscov <*name*> --meg and/or --eeg --bad <*name*> --surfsrc
+ sensor covariance fif --fwd <*name*> --out <*name*> --senscov <*name*> --noiseonly --fif --meg and/or --eeg --bad <*name*>
+ sensor covariance mat --senscov <*name*> --out <*name --bad <*name*>
+ sensor covariance eigenvalues text --senscov <*name*> --out <*name --eig --bad <*name*>
+ evoked MEG/EEG data mat --meas <*name*> --out <*name --sel <*name*> --set <*number*>
+ evoked MEG/EEG data forward model mat --meas <*name*> --fwd <*name*> --out <*name*> --bad <*name*> --set <*number*>
+ inverse operator data mat --inv <*name*> --out <*name
+ inverse operator data evoked MEG/EEG data mat --inv <*name*> --meas <*name*> --out <*name
============================================ ======== ===================================================================================== ===============================
Matlab data structures
@@ -1720,15 +1720,15 @@ The symbols employed in variable size descriptions are:
.. _BEHCICCA:
-.. table:: Matlab structures produced by mne_convert_mne_data . The prefix given with the ``--tag`` option is indicated <tag> , see :ref:`BEHCICCF`. Its default value is MNE.
+.. table:: Matlab structures produced by mne_convert_mne_data . The prefix given with the ``--tag`` option is indicated <*tag*> , see :ref:`BEHCICCF`. Its default value is MNE.
=============== =======================================
Structure Contents
=============== =======================================
- <tag> _meas Measured data
- <tag> _inv The inverse operator decomposition
- <tag> _fwd The forward solution
- <tag> _noise A standalone noise-covariance matrix
+ <*tag*> _meas Measured data
+ <*tag*> _inv The inverse operator decomposition
+ <*tag*> _fwd The forward solution
+ <*tag*> _noise A standalone noise-covariance matrix
=============== =======================================
.. _BABCBIGF:
@@ -1794,11 +1794,11 @@ following command-line options:
List the command-line options.
-**\---raw <name>**
+**\---raw <*name*>**
Specifies the name of the raw data fif file to convert.
-**\---mat <name>**
+**\---mat <*name*>**
Specifies the name of the destination Matlab file.
@@ -1807,33 +1807,33 @@ following command-line options:
With this option present, only information about the raw data file
is included. The raw data itself is omitted.
-**\---sel <name>**
+**\---sel <*name*>**
Specifies a text file which contains the names of the channels to include
in the output file, one channel name per line. If the ``--info`` option
is specified, ``--sel`` does not have any effect.
-**\---tag <tag>**
+**\---tag <*tag*>**
By default, all Matlab variables included in the output file start
- with MNE_. This option changes the prefix to <tag> _.
+ with MNE_. This option changes the prefix to <*tag*> _.
Matlab data structures
======================
The Matlab files output by mne_raw2mat can
-contain two data structures, <tag>_raw and <tag>_raw_info .
+contain two data structures, <*tag*>_raw and <*tag*>_raw_info .
If ``--info`` option is specifed, the file contains the
latter structure only.
-The <tag>_raw stucture
+The <*tag*>_raw stucture
contains only one field, data which
is a matrix containing the raw data. Each row of this matrix constitutes
the data from one channel in the original file. The data type of
this matrix is the same of the original data (2-byte signed integer,
4-byte signed integer, or single-precision float).
-The fields of the <tag>_raw_info structure
+The fields of the <*tag*>_raw_info structure
are listed in :ref:`BEHFDCIH`. Further explanation of the bufs field
is provided in :ref:`BEHJEIHJ`.
@@ -1902,23 +1902,23 @@ the following command-line options are:
List the command-line options.
-**\---raw <name>**
+**\---raw <*name*>**
Specifies the name of the raw data fif file to use as input.
-**\---mat <name>**
+**\---mat <*name*>**
Specifies the name of the destination file. Anything following the last
period in the file name will be removed before composing the output
- file name. The binary epoch file will be called <trimmed name> ``.epochs`` and
- the corresponding Matlab description file will be <trimmed name> ``_desc.mat`` .
+ file name. The binary epoch file will be called <*trimmed name*> ``.epochs`` and
+ the corresponding Matlab description file will be <*trimmed name*> ``_desc.mat`` .
-**\---tag <tag>**
+**\---tag <*tag*>**
By default, all Matlab variables included in the description file
- start with MNE_. This option changes the prefix to <tag> _.
+ start with MNE_. This option changes the prefix to <*tag*> _.
-**\---events <name>**
+**\---events <*name*>**
The file containing the event definitions. This can be a text or
fif format file produced by mne_process_raw or mne_browse_raw ,
@@ -1928,19 +1928,19 @@ the following command-line options are:
file or a fif format event file produced automatically by mne_process_raw or mne_browse_raw is
consulted for event information.
-**\---event <name>**
+**\---event <*name*>**
Event number identifying the epochs of interest.
-**\---tmin <time/ms>**
+**\---tmin <*time/ms*>**
The starting point of the epoch with respect to the event of interest.
-**\---tmax <time/ms>**
+**\---tmax <*time/ms*>**
The endpoint of the epoch with respect to the event of interest.
-**\---sel <name>**
+**\---sel <*name*>**
Specifies a text file which contains the names of the channels to include
in the output file, one channel name per line. If the ``--inv`` option
@@ -1949,7 +1949,7 @@ the following command-line options are:
channel can be included with the ``--includetrig`` option, described
below.
-**\---inv <name>**
+**\---inv <*name*>**
Specifies an inverse operator, which will be employed in two ways. First,
the channels included to output will be those included in the inverse
@@ -1957,13 +1957,13 @@ the following command-line options are:
the inverse operator file will be applied to the data. This option
cancels the effect of ``--sel`` and ``--proj`` options.
-**\---digtrig <name>**
+**\---digtrig <*name*>**
Name of the composite digital trigger channel. The default value
is 'STI 014'. Underscores in the channel name
will be replaced by spaces.
-**\---digtrigmask <number>**
+**\---digtrigmask <*number*>**
Mask to be applied to the trigger channel values before considering them.
This option is useful if one wants to set some bits in a don't care
@@ -1981,7 +1981,7 @@ the following command-line options are:
This option should not be used if the trigger channel is already
included in the selection specified with the ``--sel`` option.
-**\---filtersize <size>**
+**\---filtersize <*size*>**
Adjust the length of the FFT to be applied in filtering. The number will
be rounded up to the next power of two. If the size is INLINE_EQUATION,
@@ -1992,7 +1992,7 @@ the following command-line options are:
length will actually be INLINE_EQUATION. The default
value is 4096.
-**\---highpass <value/Hz>**
+**\---highpass <*value/Hz*>**
Highpass filter frequency limit. If this is too low with respect
to the selected FFT length and data file sampling frequency, the
@@ -2001,17 +2001,17 @@ the following command-line options are:
data. This value can be adjusted in the interactive version of the
program. The default is 0, i.e., no highpass filter in effect.
-**\---highpassw <value/Hz>**
+**\---highpassw <*value/Hz*>**
The width of the transition band of the highpass filter. The default
is 6 frequency bins, where one bin is INLINE_EQUATION.
-**\---lowpass <value/Hz>**
+**\---lowpass <*value/Hz*>**
Lowpass filter frequency limit. This value can be adjusted in the interactive
version of the program. The default is 40 Hz.
-**\---lowpassw <value/Hz>**
+**\---lowpassw <*value/Hz*>**
The width of the transition band of the lowpass filter. This value
can be adjusted in the interactive version of the program. The default
@@ -2021,7 +2021,7 @@ the following command-line options are:
Do not filter the data.
-**\---proj <name>**
+**\---proj <*name*>**
Include signal-space projection (SSP) information from this file.
If the ``--inv`` option is present, ``--proj`` has
@@ -2060,7 +2060,7 @@ Matlab data structures
======================
The Matlab description files output by mne_epochs2mat contain
-a data structure <tag>_epoch_info .
+a data structure <*tag*>_epoch_info .
The fields of the this structure are listed in :ref:`BEHFDCIH`.
Further explanation of the epochs member
is provided in :ref:`BEHHAGHE`.
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
index 98b975c..e204c22 100755
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -77,15 +77,15 @@ or more MRI data sets from ``$SUBJECTS_DIR/$SUBJECT/mri`` ,
by default they are T1 and brain. This default can be changed by
specifying the sets by one or more ``--mri`` options.
-The script creates the directories ``mri/`` <name> ``-neuromag/slices`` and ``mri/`` <name> ``-neuromag/sets`` .
+The script creates the directories ``mri/`` <*name*> ``-neuromag/slices`` and ``mri/`` <*name*> ``-neuromag/sets`` .
If the the input data set is in COR format, mne_setup_mri makes
-symbolic links from the COR files in the directory ``mri/`` <name> into ``mri/`` <name> ``-neuromag/slices`` ,
-and creates a corresponding fif file COR.fif in ``mri/`` <name> ``-neuromag/sets`` ..
+symbolic links from the COR files in the directory ``mri/`` <*name*> into ``mri/`` <*name*> ``-neuromag/slices`` ,
+and creates a corresponding fif file COR.fif in ``mri/`` <*name*> ``-neuromag/sets`` ..
This "description file" contains references to
the actual MRI slices.
If the input MRI data are stored in the newer mgz format,
-the file created in the ``mri/`` <name> ``-neuromag/sets`` directory
+the file created in the ``mri/`` <*name*> ``-neuromag/sets`` directory
will include the MRI pixel data as well. If available, the coordinate
transformations to allow conversion between the MRI (surface RAS)
coordinates and MNI and FreeSurfer Talairach coordinates are copied
@@ -127,12 +127,12 @@ script assumes that:
The script accepts the following options:
-**\---subject <subject>**
+**\---subject <*subject*>**
Defines the name of the subject. If the environment variable SUBJECT
is set correctly, this option is not required.
-**\---morph <name>**
+**\---morph <*name*>**
Name of a subject in SUBJECTS_DIR. If this option is present, the source
space will be first constructed for the subject defined by the --subject
@@ -144,18 +144,18 @@ The script accepts the following options:
source locations in the "morph" subject is not going
to be as uniform as it would be without morphing.
-**\---spacing <spacing/mm>**
+**\---spacing <*spacing/mm*>**
Specifies the grid spacing for the source space in mm. If not set,
a default spacing of 7 mm is used. Either the default or a 5-mm
spacing is recommended.
-**\---ico <number>**
+**\---ico <*number*>**
Instead of using the traditional method for cortical surface decimation
it is possible to create the source space using the topology of
- a recursively subdivided icosahedron (<number> > 0)
- or an octahedron (<number> < 0).
+ a recursively subdivided icosahedron (<*number*> > 0)
+ or an octahedron (<*number*> < 0).
This method uses the cortical surface inflated to a sphere as a
tool to find the appropriate vertices for the source space. The
benefit of the ``--ico`` option is that the source space
@@ -163,17 +163,17 @@ The script accepts the following options:
future versions of MNE software may be able to utilize. The number
of triangles increases by a factor of four in each subdivision,
starting from 20 triangles in an icosahedron and 8 triangles in an
- octahedron. Since the number of vertices on a closed surface is INLINE_EQUATION,
- the number of vertices in the *k*th subdivision of
- an icosahedron and an octahedron are INLINE_EQUATION and INLINE_EQUATION, respectively.
- The recommended values for <number> and
+ octahedron. Since the number of vertices on a closed surface is :math:`n_{vert} = (n_{tri} + 4)/2`,
+ the number of vertices in the *k* th subdivision of
+ an icosahedron and an octahedron are :math:`10 \cdot 4^k + 2` and :math:`4^{k + 1} + 2`, respectively.
+ The recommended values for <*number*> and
the corresponding number of source space locations are listed in :ref:`BABGCDHA`.
-**\---surface <name>**
+**\---surface <*name*>**
Name of the surface under the surf directory to be used. Defaults
to 'white'. ``mne_setup_source_space`` looks
- for files ``rh.`` <name> and ``lh.`` <name> under
+ for files ``rh.`` <*name*> and ``lh.`` <*name*> under
the ``surf`` directory.
**\---overwrite**
@@ -196,7 +196,7 @@ The script accepts the following options:
.. table:: Recommended subdivisions of an icosahedron and an octahedron for the creation of source spaces. The approximate source spacing and corresponding surface area have been calculated assuming a 1000-cm2 surface area per hemisphere.
========== ======================== ===================== ===============================
- <number> Sources per hemisphere Source spacing / mm Surface area per source / mm2
+ <*number*> Sources per hemisphere Source spacing / mm Surface area per source / mm2
========== ======================== ===================== ===============================
-5 1026 9.9 97
4 2562 6.2 39
@@ -211,22 +211,22 @@ Duck with a 5-mm spacing between the grid points, say
As a result, the following files are created into the ``bem`` directory:
-- <subject>-<spacing>- ``src.fif`` containing
+- <*subject*>-<*spacing*>- ``src.fif`` containing
the source space description in fif format.
-- <subject>-<spacing>- ``lh.pnt`` and <subject>-<spacing>- ``rh.pnt`` containing
+- <*subject*>-<*spacing*>- ``lh.pnt`` and <*subject*>-<*spacing*>- ``rh.pnt`` containing
the source space points in MRIlab compatible ascii format.
-- <subject>-<spacing>- ``lh.dip`` and <subject>-<spacing>- ``rh.dip`` containing
+- <*subject*>-<*spacing*>- ``lh.dip`` and <*subject*>-<*spacing*>- ``rh.dip`` containing
the source space points in MRIlab compatible ascii format. These
files contain 'dipoles', *i.e.*,
both source space points and cortex normal directions.
- If cortical patch statistics is requested, another source
- space file called <subject>-<spacing> ``p-src.fif`` will
+ space file called <*subject*>-<*spacing*> ``p-src.fif`` will
be created.
-.. note:: <spacing> will be the suggested source spacing in millimeters if the ``--spacing`` option is used. For source spaces based on *k*th subdivision of an icosahedron, <spacing> will be replaced by ``ico-`` k or ``oct-`` k , respectively.
+.. note:: <*spacing*> will be the suggested source spacing in millimeters if the ``--spacing`` option is used. For source spaces based on *k*th subdivision of an icosahedron, <*spacing*> will be replaced by ``ico-`` k or ``oct-`` k , respectively.
.. note:: After the geometry is set up it is possible to check that the source space points are located on the cortical surface. This can be easily done with by loading the ``COR.fif`` file from ``mri/T1/neuromag/sets`` into MRIlab and by subsequently overlaying the corresponding pnt or dip files using Import/Strings or Import/Dipoles from the File menu, respectively.
@@ -293,7 +293,7 @@ are:
.. note:: Different methods can be employed for the creation of the individual surfaces. For example, it may turn out that the watershed algorithm produces are better quality skin surface than the segmentation approach based on the FLASH images. If this is the case, ``outer_skin.surf`` can set to point to the corresponding watershed output file while the other surfaces can be picked from the FLASH segmentation data.
-.. note:: The triangulation files can include name of the subject as a prefix ``<subject name>-`` , *e.g.*, ``duck-inner_skull.surf`` .
+.. note:: The triangulation files can include name of the subject as a prefix ``<*subject name*>-`` , *e.g.*, ``duck-inner_skull.surf`` .
.. note:: The mne_convert_surface utility described in :ref:`BEHDIAJG` can be used to convert text format triangulation files into the FreeSurfer surface format.
@@ -349,7 +349,7 @@ script assumes that:
mne_setup_forward_model accepts
the following options:
-**\---subject <subject>**
+**\---subject <*subject*>**
Defines the name of the subject. This can be also accomplished
by setting the SUBJECT environment variable.
@@ -377,7 +377,7 @@ the following options:
to create the triangulations (see :ref:`BGBDEIGC`), the ``--noswap`` flag
is required. This option is ignored if ``--surf`` is specified
-**\---ico <number>**
+**\---ico <*number*>**
This option is relevant (and required) only with the ``--surf`` option and
if the surface files have been produced by the watershed algorithm.
@@ -397,31 +397,31 @@ the following options:
because of faster computation times. If this flag is specified,
the options ``--brainc`` , ``--skullc`` , and ``--scalpc`` are irrelevant.
-**\---brainc <conductivity/ S/m>**
+**\---brainc <*conductivity/ S/m*>**
Defines the brain compartment conductivity. The default value is 0.3 S/m.
-**\---skullc <conductivity/ S/m>**
+**\---skullc <*conductivity/ S/m*>**
Defines the skull compartment conductivity. The default value is 0.006 S/m
corresponding to a conductivity ratio 1/50 between the brain and
skull compartments.
-**\---scalpc <conductivity/ S/m>**
+**\---scalpc <*conductivity/ S/m*>**
Defines the brain compartment conductivity. The default value is 0.3 S/m.
-**\---innershift <value/mm>**
+**\---innershift <*value/mm*>**
Shift the inner skull surface outwards along the vertex normal directions
by this amount.
-**\---outershift <value/mm>**
+**\---outershift <*value/mm*>**
Shift the outer skull surface outwards along the vertex normal directions
by this amount.
-**\---scalpshift <value/mm>**
+**\---scalpshift <*value/mm*>**
Shift the scalp surface outwards along the vertex normal directions by
this amount.
@@ -431,25 +431,25 @@ the following options:
Omit the BEM model geometry dependent data preparation step. This
can be done later by running mne_setup_forward_model without the ``--nosol`` option.
-**\---model <name>**
+**\---model <*name*>**
Name for the BEM model geometry file. The model will be created into
- the directory bem as <name>- ``bem.fif`` . If
+ the directory bem as <*name*>- ``bem.fif`` . If
this option is missing, standard model names will be used (see below).
As a result of running the mne_setup_foward_model script, the
following files are created into the ``bem`` directory:
-- BEM model geometry specifications <subject>-<ntri-scalp>-<ntri-outer_skull>-<ntri-inner_skull>- ``bem.fif`` or <subject>-<ntri-inner_skull> ``-bem.fif`` containing
+- BEM model geometry specifications <*subject*>-<*ntri-scalp*>-<*ntri-outer_skull*>-<*ntri-inner_skull*>- ``bem.fif`` or <*subject*>-<*ntri-inner_skull*> ``-bem.fif`` containing
the BEM geometry in fif format. The latter file is created if ``--homog``
- option is specified. Here, <ntri-xxx> indicates
+ option is specified. Here, <*ntri-xxx*> indicates
the number of triangles on the corresponding surface.
-- <subject>-<surface name>-<ntri> ``.pnt`` files
+- <*subject*>-<*surface name*>-<*ntri*> ``.pnt`` files
are created for each of the surfaces present in the BEM model. These
can be loaded to MRIlab to check the location of the surfaces.
-- <subject>-<surface name>-<ntri> ``.surf`` files
+- <*subject*>-<*surface name*>-<*ntri*> ``.surf`` files
are created for each of the surfaces present in the BEM model. These
can be loaded to tkmedit to check
the location of the surfaces.
@@ -524,7 +524,7 @@ in graph it is advisable to change the calibration factor to one.
Furthermore, the eighth bit of the trigger word is coded incorrectly
in the original raw files. Both problems can be corrected by saying:
-``mne_fix_stim14`` <raw file>
+``mne_fix_stim14`` <*raw file*>
More information about mne_fix_stim14 is
available in :ref:`CHDBFDIC`. It is recommended that this
@@ -601,7 +601,7 @@ cognitive and patient studies to speed up subsequent processing.
This can be accomplished with the mne_process_raw and mne_browse_raw software
modules. For details, see :ref:`CACFAAAJ` and :ref:`CACBDDIE`.
-.. note:: It is recommended that the original raw file is called <name>_raw.fif and the downsampled version <name>_ds_raw.fif , respectively.
+.. note:: It is recommended that the original raw file is called <*name*>_raw.fif and the downsampled version <*name*>_ds_raw.fif , respectively.
.. _BABEAEDF:
@@ -671,34 +671,34 @@ sources located on the cortex, can be calculated with help of the
convenience script mne_do_forward_solution .
This utility accepts the following options:
-**\---subject <subject>**
+**\---subject <*subject*>**
Defines the name of the subject. This can be also accomplished
by setting the SUBJECT environment variable.
-**\---src <name>**
+**\---src <*name*>**
Source space name to use. This option overrides the ``--spacing`` option. The
source space is searched first from the current working directory
- and then from ``$SUBJECTS_DIR/`` <subject> /bem.
+ and then from ``$SUBJECTS_DIR/`` <*subject*> /bem.
The source space file must be specified exactly, including the ``fif`` extension.
-**\---spacing <spacing/mm> or ``ico-`` <number or ``oct-`` <number>**
+**\---spacing <*spacing/mm*> or ``ico-`` <*number or ``oct-`` <*number*>**
This is an alternate way to specify the name of the source space
file. For example, if ``--spacing 6`` is given on the command
- line, the source space files searched for are./<subject> -6-src.fif
- and ``$SUBJECTS_DIR/$SUBJECT/`` bem/<subject> -6-src.fif.
+ line, the source space files searched for are./<*subject*> -6-src.fif
+ and ``$SUBJECTS_DIR/$SUBJECT/`` bem/<*subject*> -6-src.fif.
The first file found is used. Spacing defaults to 7 mm.
-**\---bem <name>**
+**\---bem <*name*>**
- Specifies the BEM to be used. The name of the file can be any of <name> , <name> -bem.fif, <name> -bem-sol.fif.
+ Specifies the BEM to be used. The name of the file can be any of <*name*> , <*name*> -bem.fif, <*name*> -bem-sol.fif.
The file is searched for from the current working directory and
from ``bem`` . If this option is omitted, the most recent
BEM file in the ``bem`` directory is used.
-**\---mri <name>**
+**\---mri <*name*>**
The name of the MRI description file containing the MEG/MRI coordinate
transformation. This file was saved as part of the alignment procedure
@@ -707,14 +707,14 @@ This utility accepts the following options:
The search order for MEG/MRI coordinate transformations is discussed
below.
-**\---trans <name>**
+**\---trans <*name*>**
The name of a text file containing the 4 x 4 matrix for the coordinate transformation
from head to mri coordinates, see below. If the option ``--trans`` is
present, the ``--mri`` option is not required. The search
order for MEG/MRI coordinate transformations is discussed below.
-**\---meas <name>**
+**\---meas <*name*>**
This file is the measurement fif file or an off-line average file
produced thereof. It is recommended that the average file is employed for
@@ -723,21 +723,21 @@ This utility accepts the following options:
EEG electrode locations as well as the coordinate transformation between
the MEG device coordinates and MEG head-based coordinates.
-**\---fwd <name>**
+**\---fwd <*name*>**
This file will contain the forward solution as well as the coordinate transformations,
sensor and electrode location information, and the source space
- data. A name of the form <name> ``-fwd.fif`` is
+ data. A name of the form <*name*> ``-fwd.fif`` is
recommended. If this option is omitted the forward solution file
name is automatically created from the measurement file name and
the source space name.
-**\---destdir <directory>**
+**\---destdir <*directory*>**
Optionally specifies a directory where the forward solution will
be stored.
-**\---mindist <dist/mm>**
+**\---mindist <*dist/mm*>**
Omit source space points closer than this value to the inner skull surface.
Any source space points outside the inner skull surface are automatically
@@ -858,7 +858,7 @@ ways:
data used for this purpose should be free of technical artifacts
and epileptic activity of interest. The length of the data segment
employed should be at least 20 seconds. One can also use a long
- (> 200 s) segment of data with epileptic spikes present provided
+ (*> 200 s) segment of data with epileptic spikes present provided
that the spikes occur infrequently and that the segment is apparently
stationary with respect to background brain activity.
@@ -887,7 +887,7 @@ appropriate options, derived from the command line of mne_do_inverse_operator .
mne_do_inverse_operator assumes
the following options:
-**\---fwd <name of the forward solution file>**
+**\---fwd <*name of the forward solution file*>**
This is the forward solution file produced in the computations step described
in :ref:`BABCHEJD`.
@@ -908,12 +908,12 @@ the following options:
the source orientations are not constrained. If ``--fixed`` is specified,
the ``--loose`` flag is ignored.
-**\---loose <amount>**
+**\---loose <*amount*>**
Use a 'loose' orientation constraint. This means
that the source covariance matrix entries corresponding to the current
component normal to the cortex are set equal to one and the transverse
- components are set to <amount> .
+ components are set to <*amount*> .
Recommended value of amount is 0.1...0.6.
**\---depth**
@@ -921,7 +921,7 @@ the following options:
Employ depth weighting with the standard settings. For details,
see :ref:`CBBDFJIE` and :ref:`CBBDDBGF`.
-**\---bad <name>**
+**\---bad <*name*>**
Specifies a text file to designate bad channels, listed one channel name
(like MEG 1933) on each line of the file. Be sure to include both
@@ -932,12 +932,12 @@ the following options:
be automatically included. Also, any bad channel information in
the noise-covariance matrix file will be included.
-**\---noisecov <name>**
+**\---noisecov <*name*>**
Name of the noise-covariance matrix file computed with one of the methods
described in :ref:`BABDEEEB`. By default, the script looks
for a file whose name is derived from the forward solution file
- by replacing its ending ``-`` <anything> ``-fwd.fif`` by ``-cov.fif`` .
+ by replacing its ending ``-`` <*anything*> ``-fwd.fif`` by ``-cov.fif`` .
If this file contains a projection operator, which will automatically
attached to the noise-covariance matrix by mne_browse_raw and mne_process_raw ,
no ``--proj`` option is necessary because mne_inverse_operator will
@@ -945,17 +945,17 @@ the following options:
file. For backward compatibility, --senscov can be used as a synonym
for --noisecov.
-**\---noiserank <value>**
+**\---noiserank <*value*>**
Specifies the rank of the noise covariance matrix explicitly rather than
trying to reduce it automatically. This option is sheldom needed,
-**\---megreg <value>**
+**\---megreg <*value*>**
Regularize the MEG part of the noise-covariance matrix by this amount.
Suitable values are in the range 0.05...0.2. For details, see :ref:`CBBHEGAB`.
-**\---eegreg <value>**
+**\---eegreg <*value*>**
Like ``--megreg`` but applies to the EEG channels.
@@ -964,7 +964,7 @@ the following options:
Omit the off-diagonal terms of the noise covariance matrix. This option
is irrelevant to most users.
-**\---fmri <name>**
+**\---fmri <*name*>**
With help of this w file, an *a priori* weighting
can be applied to the source covariance matrix. The source of the weighting
@@ -975,11 +975,11 @@ the following options:
with mne_smooth_w to contain
nonzero values at all vertices of the triangular tessellation of
the cortical surface. The name of the file given is used as a stem of
- the w files. The actual files should be called <name> ``-lh.pri`` and <name> ``-rh.pri`` for
+ the w files. The actual files should be called <*name*> ``-lh.pri`` and <*name*> ``-rh.pri`` for
the left and right hemisphere weight files, respectively. The application
of the weighting is discussed in :ref:`CBBDIJHI`.
-**\---fmrithresh <value>**
+**\---fmrithresh <*value*>**
This option is mandatory and has an effect only if a weighting function
has been specified with the ``--fmri`` option. If the value
@@ -988,31 +988,31 @@ the following options:
values are multiplied by the value specified with the ``--fmrioff`` option
(default 0.1). Otherwise it is left unchanged.
-**\---fmrioff <value>**
+**\---fmrioff <*value*>**
The value by which the source covariance elements are multiplied
if the *a priori* weight falls below the threshold
set with ``--fmrithresh`` , see above.
-**\---srccov <name>**
+**\---srccov <*name*>**
Use this diagonal source covariance matrix. By default the source covariance
matrix is a multiple of the identity matrix. This option is irrelevant
to most users.
-**\---proj <name>**
+**\---proj <*name*>**
Include signal-space projection information from this file.
-**\---inv <name>**
+**\---inv <*name*>**
Save the inverse operator decomposition here. By default, the script looks
for a file whose name is derived from the forward solution file by
- replacing its ending ``-fwd.fif`` by <options> ``-inv.fif`` , where
- <options> includes options ``--meg``, ``--eeg``, and ``--fixed`` with the double
+ replacing its ending ``-fwd.fif`` by <*options*> ``-inv.fif`` , where
+ <*options*> includes options ``--meg``, ``--eeg``, and ``--fixed`` with the double
dashes replaced by single ones.
-**\---destdir <directory>**
+**\---destdir <*directory*>**
Optionally specifies a directory where the inverse operator will
be stored.
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index 1a2eb93..35860fd 100755
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -243,14 +243,14 @@ The command-line options are:
List the command-line options.
-**\---subject <name>**
+**\---subject <*name*>**
Name of the subject in SUBJECTS_DIR. In the absense of this option,
the SUBJECT environment variable will be consulted. If it is not
defined, mne_setup_source_space exits
with an error.
-**\---morph <name>**
+**\---morph <*name*>**
Name of a subject in SUBJECTS_DIR. If this option is present, the source
space will be first constructed for the subject defined by the --subject
@@ -262,21 +262,21 @@ The command-line options are:
source locations in the "morph" subject is not going
to be as uniform as it would be without morphing.
-**\---surf <name1>:<name2>:...**
+**\---surf <*name1*>: <*name2*>:...**
FreeSurfer surface file names specifying the source surfaces, separated
by colons.
-**\---spacing <spacing/mm>**
+**\---spacing <*spacing/mm*>**
Specifies the approximate grid spacing of the source space in mm.
-**\---ico <number>**
+**\---ico <*number*>**
Instead of using the traditional method for cortical surface decimation
it is possible to create the source space using the topology of
- a recursively subdivided icosahedron (<number> > 0)
- or an octahedron (<number> < 0).
+ a recursively subdivided icosahedron ( <*number*> > 0)
+ or an octahedron ( <*number*> < 0).
This method uses the cortical surface inflated to a sphere as a
tool to find the appropriate vertices for the source space. The
benefit of the ``--ico`` option is that the source space will have triangulation
@@ -288,7 +288,7 @@ The command-line options are:
is INLINE_EQUATION, the number of vertices in
the *k*th subdivision of an icosahedron and an
octahedron are INLINE_EQUATION and INLINE_EQUATION,
- respectively. The recommended values for <number> and
+ respectively. The recommended values for <*number*> and
the corresponding number of source space locations are listed in Table 3.1.
**\---all**
@@ -299,9 +299,9 @@ The command-line options are:
triangulation. This option is always recommended to include complete
information.
-**\---src <name>**
+**\---src <*name*>**
- Output file name. Use a name *<dir>/<name>*-src.fif
+ Output file name. Use a name * <*dir*>/ <*name*>*-src.fif
.. note:: If both ``--ico`` and ``--spacing`` options are present the later one on the command line takes precedence.
@@ -328,49 +328,49 @@ The command-line options are:
List the command-line options.
-**\---surf <name>**
+**\---surf <*name*>**
Specifies a FreeSurfer surface file containing the surface which
will be used as the boundary for the source space.
-**\---bem <name>**
+**\---bem <*name*>**
Specifies a BEM file (ending in ``-bem.fif`` ). The inner
skull surface will be used as the boundary for the source space.
-**\---origin <x/mm> :<y/mm> :<z/mm>**
+**\---origin <*x/mm*> : <*y/mm*> : <*z/mm*>**
If neither of the two surface options described above is present,
the source space will be spherical with the origin at this location,
given in MRI (RAS) coordinates.
-**\---rad <radius/mm>**
+**\---rad <*radius/mm*>**
Specifies the radius of a spherical source space. Default value
= 90 mm
-**\---grid <spacing/mm>**
+**\---grid <*spacing/mm*>**
Specifies the grid spacing in the source space.
-**\---mindist <distance/mm>**
+**\---mindist <*distance/mm*>**
Only points which are further than this distance from the bounding surface
are included. Default value = 5 mm.
-**\---exclude <distance/mm>**
+**\---exclude <*distance/mm*>**
Exclude points that are closer than this distance to the center
of mass of the bounding surface. By default, there will be no exclusion.
-**\---mri <name>**
+**\---mri <*name*>**
Specifies a MRI volume (in mgz or mgh format).
If this argument is present the output source space file will contain
a (sparse) interpolation matrix which allows mne_volume_data2mri to
create an MRI overlay file, see :ref:`BEHDEJEC`.
-**\---pos <name>**
+**\---pos <*name*>**
Specifies a name of a text file containing the source locations
and, optionally, orientations. Each line of the file should contain
@@ -393,9 +393,9 @@ The command-line options are:
Indicates that the source locations in the file defined with the ``--pos`` option
are give in meters instead of millimeters.
-**\---src <name>**
+**\---src <*name*>**
- Specifies the output file name. Use a name *<dir>/<name>*-src.fif
+ Specifies the output file name. Use a name * <*dir*>/ <*name*>*-src.fif
**\---all**
@@ -435,14 +435,14 @@ command-line options:
List the command-line options.
-**\---surf <name>**
+**\---surf <*name*>**
Specifies a FreeSurfer binary format surface file. Before specifying the
next surface (``--surf`` or ``--tri`` options)
details of the surface specification can be given with the options
listed in :ref:`BEHCDICC`.
-**\---tri <name>**
+**\---tri <*name*>**
Specifies a text format surface file. Before specifying the next
surface (``--surf`` or ``--tri`` options) details
@@ -460,7 +460,7 @@ command-line options:
In addition to the checks implied by the ``--check`` option,
check skull and skull thicknesses. For more information, see :ref:`BEHCBDDE`.
-**\---fif <name>**
+**\---fif <*name*>**
The output fif file containing the BEM. These files normally reside in
the bem subdirectory under the subject's mri data. A name
@@ -485,11 +485,11 @@ to define details for the corresponding surface.
not have any effect on the interpretation of the FreeSurfer surface
files specified with the ``--surf`` option.
-**\---sigma <value>**
+**\---sigma <*value*>**
The conductivity of the compartment inside this surface in S/m.
-**\---shift <value/mm>**
+**\---shift <*value/mm*>**
Shift the vertices of this surface by this amount, given in mm,
in the outward direction, *i.e.*, in the positive
@@ -501,12 +501,12 @@ to define details for the corresponding surface.
of millimeters. This option applies to text format files only. This
definition does not affect the units of the shift option.
-**\---id <number>**
+**\---id <*number*>**
Identification number to assign to this surface. (1 = inner skull, 3
= outer skull, 4 = scalp).
-**\---ico <number>**
+**\---ico <*number*>**
Downsample the surface to the designated subdivision of an icosahedron.
This option is relevant (and required) only if the triangulation
@@ -524,11 +524,11 @@ Tessellation file format
The format of the text format surface files is the following:
-<nvert> <vertex 1> <vertex 2>
-...<vertex nvert> <ntri> <triangle 1> <triangle 2>
-...<triangle ntri> ,
+ <*nvert*> <*vertex 1*> <*vertex 2*>
+... <*vertex nvert*> <*ntri*> <*triangle 1*> <*triangle 2*>
+... <*triangle ntri*> ,
-where <nvert> and <ntri> are
+where <*nvert*> and <*ntri*> are
the number of vertices and number of triangles in the tessellation,
respectively.
@@ -603,7 +603,7 @@ the geometry information for BEM. This utility is usually invoked
by the convenience script mne_setup_forward_model ,
see :ref:`CIHDBFEG`. The command-line options are:
-**\---bem <name>**
+**\---bem <*name*>**
Specify the name of the file containing the triangulations of the BEM
surfaces and the conductivities of the compartments. The standard
@@ -611,15 +611,15 @@ see :ref:`CIHDBFEG`. The command-line options are:
either with the utility mne_surf2bem (:ref:`BEHCACCJ`) or the convenience script mne_setup_forward_model ,
see :ref:`CIHDBFEG`.
-**\---sol <name>**
+**\---sol <*name*>**
Specify the name of the file containing the triangulation and conductivity
information together with the BEM geometry matrix computed by mne_prepare_bem_model .
The standard ending for this file is ``-bem-sol.fif`` .
-**\---method <approximation method>**
+**\---method <*approximation method*>**
- Select the BEM approach. If <approximation method> is ``constant`` ,
+ Select the BEM approach. If <*approximation method*> is ``constant`` ,
the BEM basis functions are constant functions on each triangle
and the collocation points are the midpoints of the triangles. With ``linear`` ,
the BEM basis functions are linear functions on each triangle and
@@ -866,25 +866,25 @@ $MNE_ROOT/share/mne/coil_def.dat. In this file, any lines starting
with the pound sign (#) are comments. A coil definition starts with
a description line containing the following fields:
-**<class>**
+** <*class*>**
This is a number indicating class of this coil. Possible values
are listed in :ref:`BJEFABHA`.
-**<id>**
+** <*id*>**
Coil id value. This value is listed in the first column of Tables :ref:`BGBBHGEC` and :ref:`CHDBDFJE`.
-**<accuracy>**
+** <*accuracy*>**
The coil representation accuracy. Possible values and their meanings
are listed in :ref:`BJEHIBJC`.
-**<np>**
+** <*np*>**
Number of integration points in this representation.
-**<size/m>**
+** <*size/m*>**
The size of the coil. For circular coils this is the diameter of
the coil and for square ones the side length of the square. This
@@ -892,14 +892,14 @@ a description line containing the following fields:
geometry. It should not be employed to infer a coil approximation
for the forward calculations.
-**<baseline/m>**
+** <*baseline/m*>**
The baseline of a this kind of a coil. This will be zero for magnetometer
coils. This information is mainly included to facilitate drawing
of the coil geometry. It should not be employed to infer a coil
approximation for the forward calculations.
-**<description>**
+** <*description*>**
Short description of this kind of a coil. If the description contains several
words, it is enclosed in quotes.
@@ -934,15 +934,15 @@ a description line containing the following fields:
Each coil description line is followed by one or more integration
point lines, consisting of seven numbers:
-**<weight>**
+** <*weight*>**
Gives the weight for this integration point (last column in Tables :ref:`BGBBHGEC` and :ref:`CHDBDFJE`).
-**<x/m> <y/m> <z/m>**
+** <*x/m*> <*y/m*> <*z/m*>**
Indicates the location of the integration point (fourth column in Tables :ref:`BGBBHGEC` and :ref:`CHDBDFJE`).
-**<nx> <ny> <nz>**
+** <*nx*> <*ny*> <*nz*>**
Components of a unit vector indicating the field component to be selected.
Note that listing a separate unit vector for each integration points
@@ -985,13 +985,13 @@ Command line options
mne_forward_solution accepts
the following command-line options:
-**\---src <name>**
+**\---src <*name*>**
Source space name to use. The name of the file must be specified exactly,
including the directory. Typically, the source space files reside
in $SUBJECTS_DIR/$SUBJECT/bem.
-**\---bem <name>**
+**\---bem <*name*>**
Specifies the BEM to be used. These files end with bem.fif or bem-sol.fif and
reside in $SUBJECTS_DIR/$SUBJECT/bem. The former file contains only
@@ -1000,27 +1000,27 @@ the following command-line options:
see :ref:`CHDJFHEB`. If precomputed geometry is not available,
the linear collocation solution will be computed by mne_forward_solution .
-**\---origin <x/mm> :<x/mm> :<z/mm>**
+**\---origin <*x/mm*> : <*x/mm*> : <*z/mm*>**
Indicates that the sphere model should be used in the forward calculations.
The origin is specified in MEG head coordinates unless the ``--mricoord`` option
is present. The MEG sphere model solution computed using the analytical
Sarvas formula. For EEG, an approximative solution described in
-**\---eegmodels <name>**
+**\---eegmodels <*name*>**
This option is significant only if the sphere model is used and
EEG channels are present. The specified file contains specifications
of the EEG sphere model layer structures as detailed in :ref:`CHDIAFIG`. If this option is absent the file ``$HOME/.mne/EEG_models`` will
be consulted if it exists.
-**\---eegmodel <model name>**
+**\---eegmodel <*model name*>**
Specifies the name of the sphere model to be used for EEG. If this option
is missing, the model Default will
be employed, see :ref:`CHDIAFIG`.
-**\---eegrad <radius/mm>**
+**\---eegrad <*radius/mm*>**
Specifies the radius of the outermost surface (scalp) of the EEG sphere
model, see :ref:`CHDIAFIG`. The default value is 90 mm.
@@ -1045,7 +1045,7 @@ the following command-line options:
Compute the forward solution for all vertices on the source space.
-**\---label <name>**
+**\---label <*name*>**
Compute the solution only for points within the specified label. Multiple
labels can be present. The label files should end with ``-lh.label`` or ``-rh.label`` for
@@ -1053,7 +1053,7 @@ the following command-line options:
is present, all surface points falling within the labels are included.
Otherwise, only decimated points with in the label are selected.
-**\---mindist <dist/mm>**
+**\---mindist <*dist/mm*>**
Omit source space points closer than this value to the inner skull surface.
Any source space points outside the inner skull surface are automatically
@@ -1065,18 +1065,18 @@ the following command-line options:
value should be about equal to the wish for the side length of the
triangles.
-**\---mindistout <name>**
+**\---mindistout <*name*>**
Specifies a file name to contain the coordinates of source space points
omitted due to the ``--mindist`` option.
-**\---mri <name>**
+**\---mri <*name*>**
The name of the MRI description file containing the MEG/MRI coordinate
transformation. This file was saved as part of the alignment procedure
outlined in :ref:`CHDBEHDC`. These files typically reside in ``$SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets`` .
-**\---trans <name>**
+**\---trans <*name*>**
The name of a text file containing the 4 x 4 matrix for the coordinate transformation
from head to mri coordinates. With ``--trans``, ``--mri`` option is not
@@ -1101,7 +1101,7 @@ the following command-line options:
MEG head coordinate system. This option is useful only in special
circumstances.
-**\---meas <name>**
+**\---meas <*name*>**
This file is the measurement fif file or an off-line average file
produced thereof. It is recommended that the average file is employed for
@@ -1110,11 +1110,11 @@ the following command-line options:
EEG electrode locations as well as the coordinate transformation between
the MEG device coordinates and MEG head-based coordinates.
-**\---fwd <name>**
+**\---fwd <*name*>**
This file will contain the forward solution as well as the coordinate transformations,
sensor and electrode location information, and the source space
- data. A name of the form <name>-fwd.fif is
+ data. A name of the form <*name*>-fwd.fif is
recommended.
**\---meg**
@@ -1161,7 +1161,7 @@ The EEG sphere model definition files may contain comment
lines starting with a # and model
definition lines in the following format:
-<name>:<radius1>:<conductivity1>:<radius2>:<conductivity2>:...
+ <*name*>: <*radius1*>: <*conductivity1*>: <*radius2*>: <*conductivity2*>:...
When the file is loaded the layers are sorted so that the
radiuses will be in ascending order and the radius of the outermost
@@ -1267,7 +1267,7 @@ the following command-line options:
List the command-line options.
-**\---fwd <name> :[<weight> ]**
+**\---fwd <*name*> :[ <*weight*> ]**
Specifies a forward solution to include. If no weight is specified,
1.0 is asssumed. In the averaging process the weights are divided
@@ -1275,6 +1275,6 @@ the following command-line options:
and their spefied weights are 2 and 3, the average is formed with
a weight of 2/5 for the first solution and 3/5 for the second one.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output file which will contain the averaged forward solution.
diff --git a/doc/source/manual/intro.rst b/doc/source/manual/intro.rst
index b5e5cc7..46a37b6 100755
--- a/doc/source/manual/intro.rst
+++ b/doc/source/manual/intro.rst
@@ -31,7 +31,7 @@ a software installation and configuration guide, :ref:`BGBDEIGC` summarizes
the software history, and :ref:`BGBDEIGC` contains the End-User
License Agreement.
-.. note:: The most recent version of this manual is available at ``$MNE_ROOT/share/doc/MNE-manual-`` <version> ``.pdf`` . For the present manual, <version> = ``2.7`` . For definition of the ``MNE_ROOT`` environment variable, see :ref:`CIHCDHGI`.
+.. note:: The most recent version of this manual is available at ``$MNE_ROOT/share/doc/MNE-manual-`` <*version*> ``.pdf`` . For the present manual, <*version*> = ``2.7`` . For definition of the ``MNE_ROOT`` environment variable, see :ref:`CIHCDHGI`.
We want to thank all MNE Software users at the Martinos Center and
in other institutions for their collaboration during the creation
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index f1f093e..ffbeaab 100755
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -337,10 +337,10 @@ In most cases, however, you can easily fit the commands listed in
this manual on one line and thus omit the backslashes. The order
of options is irrelevant. Entries to be typed literally are shown
like ``this`` . *Italicized* text indicates
-conceptual entries. For example, *<dir>* indicates a directory
+conceptual entries. For example, *<*dir*>* indicates a directory
name.
-In the description of interactive software modules the notation <menu>/<item> is
+In the description of interactive software modules the notation <*menu*>/<*item*> is
often used to denotes menu selections. For example, File/Quit stands
for the Quit button in the File menu.
@@ -384,10 +384,10 @@ by saying
If the output indicates a POSIX shell (bash or sh) you should issue
the three commands:
-``export MNE_ROOT=`` <MNE> ``export MATLAB_ROOT=`` <Matlab> ``. $MNE_ROOT/bin/mne_setup_sh``
+``export MNE_ROOT=`` <*MNE*> ``export MATLAB_ROOT=`` <*Matlab*> ``. $MNE_ROOT/bin/mne_setup_sh``
-with <MNE> replaced
-by the directory where you have installed the MNE software and <Matlab> is
+with <*MNE*> replaced
+by the directory where you have installed the MNE software and <*Matlab*> is
the directory where Matlab is installed. If you do not have Matlab,
leave MATLAB_ROOT undefined. If Matlab is not available, the utilities
mne_convert_mne_data , mne_epochs2mat , mne_raw2mat ,
@@ -395,7 +395,7 @@ and mne_simu will not work.
For csh/tcsh the corresponding commands are:
-``setenv MNE_ROOT`` <MNE> ``setenv MATLAB_ROOT`` <Matlab> ``source $MNE_ROOT/bin/mne_setup``
+``setenv MNE_ROOT`` <*MNE*> ``setenv MATLAB_ROOT`` <*Matlab*> ``source $MNE_ROOT/bin/mne_setup``
For BEM mesh generation using the watershed algorithm or
on the basis of multi-echo FLASH MRI data (see :ref:`BGBDEIGC`) and
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index cc0c92f..68c601e 100755
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -477,7 +477,7 @@ The documented structures are:
========== =========== ============================================================
Field Data type Description
========== =========== ============================================================
- version int32 The fif file version (major << 16 | minor).
+ version int32 The fif file version (major < < 16 | minor).
machid int32(2) Unique identifier of the computer this id was created on.
secs int32 Time since January 1, 1970 (seconds).
usecs int32 Time since January 1, 1970 (microseconds past secs ).
@@ -716,4 +716,4 @@ The documented structures are:
On-line documentation for individual routines
#############################################
-Each of the routines listed in Tables :ref:`BGBCGHAG` - :ref:`BGBEFADJ` has on-line documentation accessible by saying ``help`` <routine name> in Matlab.
+Each of the routines listed in Tables :ref:`BGBCGHAG` - :ref:`BGBEFADJ` has on-line documentation accessible by saying ``help`` <*routine name*> in Matlab.
diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst
index d3637bc..aff2b13 100755
--- a/doc/source/manual/mne.rst
+++ b/doc/source/manual/mne.rst
@@ -464,51 +464,51 @@ The command-line options of ``mne_inverse_operator`` are:
Use fixed source orientations normal to the cortical mantle. By default,
the source orientations are not constrained.
-**\---loose <amount>**
+**\---loose <*amount*>**
Employ a loose orientation constraint (LOC). This means that the source
covariance matrix entries corresponding to the current component
normal to the cortex are set equal to one and the transverse components
- are set to <amount> . Recommended
+ are set to <*amount*> . Recommended
value of amount is 0.2...0.6.
-**\---loosevar <amount>**
+**\---loosevar <*amount*>**
Use an adaptive loose orientation constraint. This option can be
only employed if the source spaces included in the forward solution
have the patch information computed, see :ref:`CIHCHDAE`. Blaa
blaa...***what???**
-**\---fwd <name>**
+**\---fwd <*name*>**
Specifies the name of the forward solution to use.
-**\---noisecov <name>**
+**\---noisecov <*name*>**
Specifies the name of the noise-covariance matrix to use. If this
file contains a projection operator, attached by mne_browse_raw and mne_process_raw ,
no additional projection vectors can be added with the ``--proj`` option. For
backward compatibility, ``--senscov`` can be used as a synonym for ``--noisecov``.
-**\---noiserank <value>**
+**\---noiserank <*value*>**
Specifies the rank of the noise covariance matrix explicitly rather than
trying to reduce it automatically. This option is seldom needed,
-**\---gradreg <value>**
+**\---gradreg <*value*>**
Regularize the planar gradiometer section (channels for which the unit
of measurement is T/m) of the noise-covariance matrix by the given
amount. The value is restricted to the range 0...1. For details, see :ref:`CBBHEGAB`.
-**\---magreg <value>**
+**\---magreg <*value*>**
Regularize the magnetometer and axial gradiometer section (channels
for which the unit of measurement is T) of the noise-covariance matrix
by the given amount. The value is restricted to the range 0...1.
For details, see :ref:`CBBHEGAB`.
-**\---eegreg <value>**
+**\---eegreg <*value*>**
Regularize the EEG section of the noise-covariance matrix by the given
amount. The value is restricted to the range 0...1. For details, see :ref:`CBBHEGAB`.
@@ -520,7 +520,7 @@ The command-line options of ``mne_inverse_operator`` are:
data has been insufficient to calculate a reliable estimate of the
full noise-covariance matrix.
-**\---srccov <name>**
+**\---srccov <*name*>**
Specifies the name of the diagonal source-covariance matrix to use.
By default the source covariance matrix is a multiple of the identity matrix.
@@ -532,17 +532,17 @@ The command-line options of ``mne_inverse_operator`` are:
Employ depth weighting. For details, see :ref:`CBBDFJIE`.
-**\---weightexp <value>**
+**\---weightexp <*value*>**
This parameter determines the steepness of the depth weighting function
(default = 0.8). For details, see :ref:`CBBDFJIE`.
-**\---weightlimit <value>**
+**\---weightlimit <*value*>**
Maximum relative strength of the depth weighting (default = 10). For
details, see :ref:`CBBDFJIE`.
-**\---fmri <name>**
+**\---fmri <*name*>**
With help of this w file, an *a priori* weighting
can be applied to the source covariance matrix. The source of the
@@ -553,11 +553,11 @@ The command-line options of ``mne_inverse_operator`` are:
with mne_smooth_w to contain
nonzero values at all vertices of the triangular tessellation of
the cortical surface. The name of the file given is used as a stem of
- the w files. The actual files should be called <name> ``-lh.pri`` and <name> ``-rh.pri`` for
+ the w files. The actual files should be called <*name*> ``-lh.pri`` and <*name*> ``-rh.pri`` for
the left and right hemsphere weight files, respectively. The application
of the weighting is discussed in :ref:`CBBDIJHI`.
-**\---fmrithresh <value>**
+**\---fmrithresh <*value*>**
This option is mandatory and has an effect only if a weighting function
has been specified with the ``--fmri`` option. If the value
@@ -566,13 +566,13 @@ The command-line options of ``mne_inverse_operator`` are:
values are multiplied by the value specified with the ``--fmrioff`` option
(default 0.1). Otherwise it is left unchanged.
-**\---fmrioff <value>**
+**\---fmrioff <*value*>**
The value by which the source covariance elements are multiplied
if the *a priori* weight falls below the threshold
set with ``--fmrithresh`` , see above.
-**\---bad <name>**
+**\---bad <*name*>**
A text file to designate bad channels, listed one channel name on each
line of the file. If the noise-covariance matrix specified with the ``--noisecov`` option
@@ -598,7 +598,7 @@ The command-line options of ``mne_inverse_operator`` are:
location is used. If the ``--loose`` or ``--loosevar`` option
is employed, ``--surfsrc`` is implied.
-**\---exclude <name>**
+**\---exclude <*name*>**
Exclude the source space points defined by the given FreeSurfer 'label' file
from the source reconstruction. This is accomplished by setting
@@ -607,7 +607,7 @@ The command-line options of ``mne_inverse_operator`` are:
if it refers to the left hemisphere and with ``-rh.label`` if
it lists points in the right hemisphere, respectively.
-**\---proj <name>**
+**\---proj <*name*>**
Include signal-space projection (SSP) information from this file. For information
on SSP, see :ref:`CACCHABI`. If the projections are present in
@@ -625,7 +625,7 @@ The command-line options of ``mne_inverse_operator`` are:
For technical details of the patch information, please consult :ref:`CBBDBHDI`. This option is considered experimental at
the moment.
-**\---inv <name>**
+**\---inv <*name*>**
Save the inverse operator decomposition here.
@@ -661,49 +661,49 @@ General options
Input files
===========
-**\---inv <name>**
+**\---inv <*name*>**
Load the inverse operator decomposition from here.
-**\---meas <name>**
+**\---meas <*name*>**
Load the MEG or EEG data from this file.
-**\---set <number>**
+**\---set <*number*>**
The data set (condition) number to load. This is the sequential
number of the condition. You can easily see the association by looking
at the condition list in mne_analyze when
you load the file.
-**\---stcin <name>**
+**\---stcin <*name*>**
Specifies an stc file to read as input.
Times and baseline
==================
-**\---tmin <time/ms>**
+**\---tmin <*time/ms*>**
Specifies the starting time employed in the analysis. If ``--tmin`` option
is missing the analysis starts from the beginning of the epoch.
-**\---tmax <time/ms>**
+**\---tmax <*time/ms*>**
Specifies the finishing time employed in the analysis. If ``--tmax`` option
is missing the analysis extends to the end of the epoch.
-**\---tstep <step/ms>**
+**\---tstep <*step/ms*>**
Time step between consequtive movie frames, specified in milliseconds.
-**\---integ < INLINE_EQUATION/ms>**
+**\---integ < INLINE_EQUATION/ms*>**
Integration time for each frame. Defaults to zero. The integration will
be performed on sensor data. If the time specified for a fram is INLINE_EQUATION,
the integration range will be INLINE_EQUATION.
-**\---pick <time/ms>**
+**\---pick <*time/ms*>**
Pick a time for the production of rgb, tif, jpg, png, or w files.
Several pick options may be present. The time must be with in the
@@ -722,17 +722,17 @@ Times and baseline
snapshots into a composite "filmstrip" reprensentation.
However, such scripts are not yet part of the MNE software.
-**\---bmin <time/ms>**
+**\---bmin <*time/ms*>**
Specifies the starting time of the baseline. In order to activate
baseline correction, both ``--bmin`` and ``--bmax`` options
must be present.
-**\---bmax <time/ms>**
+**\---bmax <*time/ms*>**
Specifies the finishing time of the baseline.
-**\---baselines <file_name>**
+**\---baselines <*file_name*>**
Specifies a file which contains the baseline settings. Each line
of the file should contain a name of a channel, followed by the
@@ -746,7 +746,7 @@ Times and baseline
Options controlling the estimates
=================================
-**\---nave <value>**
+**\---nave <*value*>**
Specifies the effective number of averaged epochs in the input data, INLINE_EQUATION,
as discussed in :ref:`CBBDGIAE`. If the input data file is
@@ -759,7 +759,7 @@ Options controlling the estimates
employing this flag or by adjusting the number of averages in the
data file with help of the utility mne_change_nave .
-**\---snr <value>**
+**\---snr <*value*>**
An estimate for the amplitude SNR. The regularization parameter will
be set as INLINE_EQUATION. The default value is
@@ -793,14 +793,14 @@ Options controlling the estimates
Visualization options
=====================
-**\---subject <subject>**
+**\---subject <*subject*>**
Specifies the subject whose MRI data is employed in the visualization.
This must be the same subject that was used for computing the current
estimates. The environment variable SUBJECTS_DIR must be set to
point to a locations where the subjects are to be found.
-**\---morph <subject>**
+**\---morph <*subject*>**
Morph the data to to the cortical surface of another subject. The Quicktime
movie, stc-file, graphics snapshot, and w-file outputs are affected
@@ -815,24 +815,24 @@ Visualization options
see :ref:`CHDBBHDH`. More information about morphing and averaging
can be found in :ref:`ch_morph`.
-**\---morphgrade <number>**
+**\---morphgrade <*number*>**
Adjusts the number of vertices in the stc files produced when morphing
is in effect. By default the number of vertices is 10242 corresponding
to --morphgrade value 5. Allowed values are 3, 4, 5, and 6 corresponding
to 642, 2562, 10242, and 40962 vertices, respectively.
-**\---surface <surface name>**
+**\---surface <*surface name*>**
Name of the surface employed in the visualization. The default is inflated .
-**\---curv <name>**
+**\---curv <*name*>**
Specify a nonstandard curvature file name. The default curvature files
are ``lh.curv`` and ``rh.curv`` . With this option,
- the names become ``lh.`` <name> and ``rh.`` <name> .
+ the names become ``lh.`` <*name*> and ``rh.`` <*name*> .
-**\---patch <name> [:<angle/deg> ]**
+**\---patch <*name*> [: <*angle/deg*> ]**
Specify the name of a surface patch to be used for visualization instead
of the complete cortical surface. A complete name of a patch file
@@ -845,17 +845,17 @@ Visualization options
before display. You can check a suitable value for the rotation
angle by loading the patch interactively in mne_analyze .
-**\---width <value>**
+**\---width <*value*>**
Width of the graphics output frames in pixels. The default width
is 600 pixels.
-**\---height <value>**
+**\---height <*value*>**
Height of the graphics output frames in pixels. The default height
is 400 pixels.
-**\---mag <factor>**
+**\---mag <*factor*>**
Magnify the the visualized scene by this factor.
@@ -869,7 +869,7 @@ Visualization options
Select the right hemisphere for graphics output. By default, both hemisphere
are processed.
-**\---view <name>**
+**\---view <*name*>**
Select the name of the view for mov, rgb, and tif graphics output files.
The default viewnames, defined in ``$MNE_ROOT/share/mne/mne_analyze/eyes`` ,
@@ -882,7 +882,7 @@ Visualization options
right hemisphere up vector. The entities are separated by semicolons.
Lines beginning with the pound sign (#) are considered to be comments.
-**\---smooth <nstep>**
+**\---smooth <*nstep*>**
Number of smoothsteps to take when producing the output frames. Depending
on the source space decimation, an appropriate number is 4 - 7.
@@ -899,7 +899,7 @@ Visualization options
Do not include the scalebar in the image output files or movies.
-**\---alpha <value>**
+**\---alpha <*value*>**
Adjust the opacity of maps shown on the cortical surface (0 = transparent,
1 = totally opaque). The default value is 1.
@@ -907,28 +907,28 @@ Visualization options
Thresholding
============
-**\---fthresh <value>**
+**\---fthresh <*value*>**
Specifies the threshold for the displayed colormaps. At the threshold,
the overlayed color will be equal to the background surface color.
For currents, the value will be multiplied byINLINE_EQUATION.
The default value is 8.
-**\---fmid <value>**
+**\---fmid <*value*>**
Specifies the midpoint for the displayed colormaps. At this value, the
overlayed color will be read (positive values) or blue (negative values).
For currents, the value will be multiplied byINLINE_EQUATION.
The default value is 15.
-**\---fmax <value>**
+**\---fmax <*value*>**
Specifies the maximum point for the displayed colormaps. At this value,
the overlayed color will bright yellow (positive values) or light
blue (negative values). For currents, the value will be multiplied
byINLINE_EQUATION. The default value is 20.
-**\---fslope <value>**
+**\---fslope <*value*>**
Included for backwards compatibility. If this option is specified
and ``--fmax`` option is *not* specified, INLINE_EQUATION.
@@ -936,81 +936,81 @@ Thresholding
Output files
============
-**\---mov <name>**
+**\---mov <*name*>**
Produce QuickTime movie files. This is the 'stem' of
the ouput file name. The actual name is derived by stripping anything
- upto and including the last period from the end of <name> .
+ upto and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` or ``-rh`` is
- then appended. The name of the view is indicated with ``-`` <viename> .
+ then appended. The name of the view is indicated with ``-`` <*viename*> .
Finally, ``.mov`` is added to indicate a QuickTime output
file. The movie is produced for all times as dictated by the ``--tmin`` , ``--tmax`` , ``--tstep`` ,
and ``--integ`` options.
-**\---qual <value>**
+**\---qual <*value*>**
Quality of the QuickTime movie output. The default quality is 80 and
allowed range is 25 - 100. The size of the movie files is a monotonously
increasing function of the movie quality.
-**\---rate <rate>**
+**\---rate <*rate*>**
Specifies the frame rate of the QuickTime movies. The default value is INLINE_EQUATION,
where INLINE_EQUATION is the time between subsequent
movie frames produced in seconds.
-**\---rgb <name>**
+**\---rgb <*name*>**
Produce rgb snapshots. This is the 'stem' of the
ouput file name. The actual name is derived by stripping anything
- upto and including the last period from the end of <name> .
+ upto and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` or ``-rh`` is
- then appended. The name of the view is indicated with ``-`` <viename> .
+ then appended. The name of the view is indicated with ``-`` <*viename*> .
Finally, ``.rgb`` is added to indicate an rgb output file.
Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
-**\---tif <name>**
+**\---tif <*name*>**
Produce tif snapshots. This is the 'stem' of the
ouput file name. The actual name is derived by stripping anything
- upto and including the last period from the end of <name> .
+ upto and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` or ``-rh`` is
- then appended. The name of the view is indicated with ``-`` <viename> .
+ then appended. The name of the view is indicated with ``-`` <*viename*> .
Finally, ``.tif`` is added to indicate an rgb output file.
Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
The tif output files are *not* compressed. Pass
the files through an image processing program to compress them.
-**\---jpg <name>**
+**\---jpg <*name*>**
Produce jpg snapshots. This is the 'stem' of the
ouput file name. The actual name is derived by stripping anything
- upto and including the last period from the end of <name> .
+ upto and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` or ``-rh`` is
- then appended. The name of the view is indicated with ``-`` <viename> .
+ then appended. The name of the view is indicated with ``-`` <*viename*> .
Finally, ``.jpg`` is added to indicate an rgb output file.
Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
-**\---png <name>**
+**\---png <*name*>**
Produce png snapshots. This is the 'stem' of the
ouput file name. The actual name is derived by stripping anything
- upto and including the last period from the end of <name> .
+ upto and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` or ``-rh`` is
- then appended. The name of the view is indicated with ``-`` <viename> .
+ then appended. The name of the view is indicated with ``-`` <*viename*> .
Finally, ``.png`` is added to indicate an rgb output file.
Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
-**\---w <name>**
+**\---w <*name*>**
Produce w file snapshots. This is the 'stem' of
the ouput file name. The actual name is derived by stripping anything
- upto and including the last period from the end of <name> .
+ upto and including the last period from the end of <*name*> .
According to the hemisphere, ``-lh`` .w or ``-rh`` .w
is then appended. Files are produced for all picked times as dictated
by the ``--pick`` and ``--integ`` options.
-**\---stc <name>**
+**\---stc <*name*>**
Produce stc files for either the original subject or the one selected with
the ``--morph`` option. These files will contain data only
@@ -1021,20 +1021,20 @@ Output files
averaged together, e.g., in Matlab since they always contain an
identical set of vertices.
-**\---norm <name>**
+**\---norm <*name*>**
Indicates that a separate w file
containing the noise-normalization values will be produced. The
option ``--spm`` must also be present. Nevertheless, the
movies and stc files output will
- contain MNE values. The noise normalization data files will be called <name>-<SNR> ``-lh.w`` and <name>-<SNR> ``-rh.w`` .
+ contain MNE values. The noise normalization data files will be called <*name*>- <*SNR*> ``-lh.w`` and <*name*>- <*SNR*> ``-rh.w`` .
.. _CBBHHCEF:
Label processing
================
-**\---label <name>**
+**\---label <*name*>**
Specifies a label file to process. For each label file, the values
of the computed estimates are listed in text files. The label files
@@ -1042,7 +1042,7 @@ Label processing
specify regions of interests (ROIs). A label file name should end
with ``-lh.label`` for left-hemisphere ROIs and with ``-rh.label`` for
right-hemisphere ones. The corresponding output files are tagged
- with ``-lh-`` <data type> ``.amp`` and ``-rh-`` <data type> ``.amp``, respectively. <data type> equals ``'mne`` ' for
+ with ``-lh-`` <*data type*> ``.amp`` and ``-rh-`` <*data type*> ``.amp``, respectively. <*data type*> equals ``'mne`` ' for
expected current data and ``'spm`` ' for
dSPM data. Each line of the output file contains the waveform of
the output quantity at one of the source locations falling inside
@@ -1069,14 +1069,14 @@ Label processing
Output the label data time by time instead of the default vertex-by-vertex
output.
-**\---labeltag <tag>**
+**\---labeltag <*tag*>**
End the output files with the specified tag. By default, the output files
will end with ``-mne.amp`` or ``-spm.amp`` depending
on whether MNE or one of the noise-normalized estimates (dSPM or sLORETA)
was selected.
-**\---labeloutdir <directory>**
+**\---labeloutdir <*directory*>**
Specifies the directory where the output files will be located.
By default, they will be in the current working directory.
@@ -1086,7 +1086,7 @@ Label processing
Include comments in the output files. The comment lines begin with the
percent sign to make the files compatible with Matlab.
-**\---scaleby <factor>**
+**\---scaleby <*factor*>**
By default, the current values output to the files will be in the
actual physical units (Am). This option allows scaling of the current
@@ -1140,34 +1140,34 @@ Command-line options
List the command-line options.
-**\---in <filename>**
+**\---in <*filename*>**
Specifies the input data file. This can be either an evoked data
file or a raw data file.
-**\---bmin <time/ms>**
+**\---bmin <*time/ms*>**
Specifies the starting time of the baseline. In order to activate
baseline correction, both ``--bmin`` and ``--bmax`` options
must be present. This option applies to evoked data only.
-**\---bmax <time/ms>**
+**\---bmax <*time/ms*>**
Specifies the finishing time of the baseline. This option applies
to evoked data only.
-**\---set <number>**
+**\---set <*number*>**
The data set (condition) number to load. This is the sequential
number of the condition. You can easily see the association by looking
at the condition list in mne_analyze when
you load the file.
-**\---inv <name>**
+**\---inv <*name*>**
Load the inverse operator decomposition from here.
-**\---nave <value>**
+**\---nave <*value*>**
Specifies the effective number of averaged epochs in the input data, INLINE_EQUATION,
as discussed in :ref:`CBBDGIAE`. If the input data file is
@@ -1180,7 +1180,7 @@ Command-line options
employing this flag or by adjusting the number of averages in the
data file with help of the utility mne_change_nave .
-**\---snr <value>**
+**\---snr <*value*>**
An estimate for the amplitude SNR. The regularization parameter will
be set as INLINE_EQUATION. The default value is
@@ -1201,7 +1201,7 @@ Command-line options
Provide source locations and orientations in the MRI coordinate frame
instead of the default head coordinate frame.
-**\---label <name>**
+**\---label <*name*>**
Specifies a label file to process. For each label file, the values
of the computed estimates stored in a fif file. For more details,
@@ -1209,7 +1209,7 @@ Command-line options
or mne_analyze and specify regions
of interests (ROIs). A label file name should end with ``-lh.label`` for
left-hemisphere ROIs and with ``-rh.label`` for right-hemisphere
- ones. The corresponding output files are tagged with ``-lh-`` <data type> ``.fif`` and ``-rh-`` <data type> ``.fif`` , respectively. <data type> equals ``'mne`` ' for expected
+ ones. The corresponding output files are tagged with ``-lh-`` <*data type*> ``.fif`` and ``-rh-`` <*data type*> ``.fif`` , respectively. <*data type*> equals ``'mne`` ' for expected
current data and ``'spm`` ' for dSPM data.
For raw data, ``_raw.fif`` is employed instead of ``.fif`` .
The output files are stored in the same directory as the label files.
@@ -1229,7 +1229,7 @@ Command-line options
flag will not have any effect if the inverse operator has been computed
with the strict orientation constraint active.
-**\---labeldir <directory>**
+**\---labeldir <*directory*>**
All previous ``--label`` options will be ignored when this
option is encountered. For each label in the directory, the output
@@ -1244,12 +1244,12 @@ Command-line options
of the label files, truncated to 15 characters, instead of names
containing the vertex numbers.
-**\---out <name>**
+**\---out <*name*>**
Required with ``--labeldir`` . This is the output file for
the data.
-**\---extra <name>**
+**\---extra <*name*>**
By default, the output includes the current estimate signals and
the digital trigger channel, see ``--digtrig`` option,
@@ -1263,13 +1263,13 @@ Command-line options
No additional channels will be included with this option present.
-**\---digtrig <name>**
+**\---digtrig <*name*>**
Name of the composite digital trigger channel. The default value
is 'STI 014'. Underscores in the channel name
will be replaced by spaces.
-**\---split <size/MB>**
+**\---split <*size/MB*>**
Specifies the maximum size of the raw data files saved. By default, the
output is split into files which are just below 2 GB so that the
@@ -1288,7 +1288,7 @@ by postprocessing software as follows:
**channel name**
- Will be set to J[xyz] <number> ,
+ Will be set to J[xyz] <*number*> ,
where the source component is indicated by the coordinat axis name
and number is the vertex number, starting from zero, in the complete
triangulation of the hemisphere in question.
diff --git a/doc/source/manual/morph.rst b/doc/source/manual/morph.rst
index cc67b2e..8a9c29f 100755
--- a/doc/source/manual/morph.rst
+++ b/doc/source/manual/morph.rst
@@ -123,14 +123,14 @@ this directory exists.
The names of the files in ``$SUBJECTS_DIR/morph-maps`` are
of the form:
-<A> -<B> -``morph.fif`` ,
+ <*A*> - <*B*> -``morph.fif`` ,
-where <A> and <B> are
+where <*A*> and <*B*> are
names of subjects. These files contain the maps for both hemispheres,
and in both directions, *i.e.*, both INLINE_EQUATION and INLINE_EQUATION, as
-defined above. Thus the files <A> -<B> -``morph.fif`` or <B> -<A> -``morph.fif`` are
+defined above. Thus the files <*A*> - <*B*> -``morph.fif`` or <*B*> - <*A*> -``morph.fif`` are
functionally equivalent. The name of the file produced by mne_analyze or mne_make_movie depends
-on the role of <A> and <B> in
+on the role of <*A*> and <*B*> in
the analysis.
If you choose to compute the morphing maps in batch in advance,
@@ -149,11 +149,11 @@ accepts the following command-line options:
Recompute the morphing maps even if they already exist.
-**\---from <subject>**
+**\---from <*subject*>**
Compute morphing maps from this subject.
-**\---to <subject>**
+**\---to <*subject*>**
Compute morphing maps to this subject.
@@ -186,25 +186,25 @@ options:
List the command-line options.
-**\---from <subject>**
+**\---from <*subject*>**
Name of the subject for which the labels were originally defined.
-**\---to <subject>**
+**\---to <*subject*>**
Name of the subject for which the morphed labels should be created.
-**\---labeldir <directory>**
+**\---labeldir <*directory*>**
A directory containing the labels to morph.
-**\---prefix <prefix>**
+**\---prefix <*prefix*>**
- Adds <prefix> in the beginning
- of the output label names. A dash will be inserted between <prefix> and
+ Adds <*prefix*> in the beginning
+ of the output label names. A dash will be inserted between <*prefix*> and
the rest of the name.
-**\---smooth <number>**
+**\---smooth <*number*>**
Apply smoothing with the indicated number of iteration steps (see :ref:`CHDEBAHH`) to the labels before morphing them. This is
advisable because otherwise the resulting labels may have little
@@ -278,7 +278,7 @@ command line arguments are:
List the command-line options.
-**\---desc <filenname>**
+**\---desc <*filenname*>**
Specifies the description file for averaging. The format of this
file is described below.
@@ -307,37 +307,37 @@ specifies the destination for the average.
The global phrases are:
-**tmin <value/ms>**
+**tmin <*value/ms*>**
The minimum time to be considered. The output stc file starts at
this time point if the time ranges of the stc files include this
time. Otherwise the output starts from the next later available
time point.
-**tstep <step/ms>**
+**tstep <*step/ms*>**
Time step between consecutive movie frames, specified in milliseconds.
-**tmax <value/ms>**
+**tmax <*value/ms*>**
The maximum time point to be considered. A multiple of tstep will be
added to the first time point selected until this value or the last time
point in one of the input stc files is reached.
-**integ < INLINE_EQUATION/ms>**
+**integ < INLINE_EQUATION/ms*>**
Integration time for each frame. Defaults to zero. The integration will
be performed on sensor data. If the time specified for a frame is INLINE_EQUATION,
the integration range will be INLINE_EQUATION.
-**stc <filename>**
+**stc <*filename*>**
Specifies an input stc file. The filename can be specified with
one of the ``-lh.stc`` and ``-rh.stc`` endings
or without them. This phrase ends the present context and starts
an input context.
-**deststc <filename>**
+**deststc <*filename*>**
Specifies the output stc file. The filename can be specified with
one of the ``-lh.stc`` and ``-rh.stc`` endings
@@ -354,7 +354,7 @@ The global phrases are:
The contextual phrases are:
-**weight <value>**
+**weight <*value*>**
Specifies the weight of the current data set. This phrase is valid
in the input and output contexts.
@@ -367,7 +367,7 @@ The contextual phrases are:
or output contexts, applies only to the data associated with that
context.
-**pow <value>**
+**pow <*value*>**
Specifies that the data should raised to the specified power. For
negative values, the absolute value of the data will be taken and
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index 17711e6..596d4a1 100755
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -63,16 +63,16 @@ To make a personal copy of the sample data set, follow these steps:
- Set up for using the MNE software as
instructed in :ref:`CIHCDHGI` of this manual.
-- Create a directory for your personal copy: ``mkdir`` <yourdir> , where <yourdir> is
+- Create a directory for your personal copy: ``mkdir`` <*yourdir*> , where <*yourdir*> is
the location where you want your personal copy to reside. Tho store
the sample data set and to finish the tutorials in this Chapter, you
- need approximately 600 MBytes of space on the disk where <yourdir> is
+ need approximately 600 MBytes of space on the disk where <*yourdir*> is
located.
-- Go to your newly created sample data directory: ``cd`` <yourdir> .
+- Go to your newly created sample data directory: ``cd`` <*yourdir*> .
-- Extract the sample data: ``tar zxvf`` <dir> ``/MNE-sample-data.tar.gz`` ,
- where <dir> is the location
+- Extract the sample data: ``tar zxvf`` <*dir*> ``/MNE-sample-data.tar.gz`` ,
+ where <*dir*> is the location
of the tar archive, provided by your system administrator.
To start the tutorials you need to:
@@ -80,21 +80,21 @@ To start the tutorials you need to:
- Set up MNE software user environment,
see :ref:`CIHCDHGI`.
-- Set the SUBJECTS_DIR environment variable:``setenv SUBJECTS_DIR`` <yourdir> ``/subjects`` (csh
- and tcsh) or ``export SUBJECTS_DIR=`` <yourdir> ``/subjects`` (POSIX-compatible
+- Set the SUBJECTS_DIR environment variable:``setenv SUBJECTS_DIR`` <*yourdir*> ``/subjects`` (csh
+ and tcsh) or ``export SUBJECTS_DIR=`` <*yourdir*> ``/subjects`` (POSIX-compatible
shell). Most users at the Martinos Center have tcsh as their login shell.
- Assign the SUBJECT environment variable the value ``sample`` .
- For convenience, you can also set the environment variable
- SAMPLE to <yourdir> . The following
+ SAMPLE to <*yourdir*> . The following
tutorial examples assume you have done this.
- Set up the FreeSurfer environment
using the commands specific to your site. The FreeSurfer license
is needed for the source space creation covered in :ref:`CHDIGEJG`.
-.. note:: From this point on, directories and files under your personal copy of the sample data set under <yourdir> will be referred to by relative pathnames. For example, the file <yourdir> ``/MEG/sample/audvis.ave`` will be simply called ``MEG/sample/audvis.ave`` .
+.. note:: From this point on, directories and files under your personal copy of the sample data set under <*yourdir*> will be referred to by relative pathnames. For example, the file <*yourdir*> ``/MEG/sample/audvis.ave`` will be simply called ``MEG/sample/audvis.ave`` .
.. note:: You can also proceed without FreeSurfer installed if you choose to use source space creation using the recursively subdivided octahedron or icosahedron method. For more information, see the Note in :ref:`CHDIGEJG`.
@@ -615,9 +615,9 @@ This will create the MRI set file in the ``$SUBJECTS_DIR/sample/mri/T1-neuromag/
which was created by mne_setup_mri_data ,
see :ref:`CHDBBAEJ`. The file will be called
-``COR-`` <username>-<date>-<time> .fif
+``COR-`` <*username*>- <*date*>- <*time*> .fif
-where <username> is
+where <*username*> is
your login name.
You can also save transformation to a fif file through the Save... button.
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
index a5f485c..831272d 100755
--- a/doc/source/manual/utilities.rst
+++ b/doc/source/manual/utilities.rst
@@ -43,7 +43,7 @@ to the standard output. The command line options for mne_show_fiff are:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies the fif file whose contents will be listed.
@@ -58,7 +58,7 @@ to the standard output. The command line options for mne_show_fiff are:
Only list the blocks (the tree structure) of the file. The tags
within each block are not listed.
-**\---indent <number>**
+**\---indent <*number*>**
Number of spaces for indentation for each deeper level in the tree structure
of the fif files. The default indentation is 3 spaces in terse and
@@ -70,7 +70,7 @@ to the standard output. The command line options for mne_show_fiff are:
This options has no effect unless the ``--verbose`` option
is also present.
-**\---tag <number>**
+**\---tag <*number*>**
List only tags of this kind. Multiple ``--tag`` options
can be specified to list several different kinds of data.
@@ -102,14 +102,14 @@ This utility adds or replaces information about unusable
List the command-line options.
-**\---bad <filename>**
+**\---bad <*filename*>**
Specify a text file containing the names of the bad channels, one channel
name per line. The names of the channels in this file must match
those in the data file exactly. If this option is missing, the bad channel
information is cleared.
-**<data file name>**
+** <*data file name*>**
The remaining arguments are taken as data file names to be modified.
@@ -133,7 +133,7 @@ when stimulus input 16 is used and the data are acquired in the
32-bit mode. This problem can be fixed by running mne_fix_stim14 on
a raw data file with the ``--32`` option:
-``mne_fix_stim14 --32`` <raw data file>
+``mne_fix_stim14 --32`` <*raw data file*>
In this case, the correction will be applied to the stimulus
channels 'STI101' and 'STI201'.
@@ -158,11 +158,11 @@ options are:
List the command-line options.
-**\---file <name>**
+**\---file <*name*>**
Specify the measurement data file to be checked or modified.
-**\---dig <name>**
+**\---dig <*name*>**
Name of the file containing the Polhemus digitizer information. Default
is the data file name.
@@ -236,11 +236,11 @@ options:
List the command-line options.
-**\---fif <name>**
+**\---fif <*name*>**
Specifies the name of the data file to modify.
-**\---alias <name>**
+**\---alias <*name*>**
Specifies the text file which contains the modifications to be applied,
see below.
@@ -307,11 +307,11 @@ the following command-line options:
List the command-line options.
-**\---raw <name>**
+**\---raw <*name*>**
Specifies the raw data file to be modified.
-**\---trg <name>**
+**\---trg <*name*>**
Specifies the trigger line modification list. This text file should
contain two entries per line: the sample number and the trigger
@@ -375,7 +375,7 @@ the following command-line options:
Remove the FIFF_SUBJ_HIS_ID tag as well, see above.
-**\---file <name>**
+**\---file <*name*>**
Specifies the name of the file to be modified.
@@ -404,13 +404,13 @@ the MNE software.
mne_copy_processing_history is
simple to use:
-``mne_copy_processing_history --from`` <from> ``--to`` <to> ,
+``mne_copy_processing_history --from`` <*from*> ``--to`` <*to*> ,
-where <from> is an
-original raw data file containing the processing history and <to> is
+where <*from*> is an
+original raw data file containing the processing history and <*to*> is
a file output with older MNE Matlab routines. Be careful: this operation
-cannot be undone. If the <from> file
-does not have the processing history block or the <to> file
+cannot be undone. If the <*from*> file
+does not have the processing history block or the <*to*> file
already has it, the destination file remains unchanged.
.. _CHDHJABJ:
@@ -450,12 +450,12 @@ the following command-line options:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies a measurement file which contains the EEG electrode locations.
This file is not modified.
-**\---inmat <name>**
+**\---inmat <*name*>**
Specifies the output file where the layout is stored. Suffix ``.lout`` is recommended
for layout files. mne_analyze and mne_browse_raw look
@@ -466,18 +466,18 @@ the following command-line options:
Indicates that the file specified with the ``--inmat`` option
contains a transpose of the derivation matrix.
-**\---thresh <value>**
+**\---thresh <*value*>**
Specifies the threshold between values to be considered zero and non-zero
in the input file specified with the ``--inmat`` option.
The default threshold is INLINE_EQUATION.
-**\---out <name>**
+**\---out <*name*>**
Specifies output fif file to contain the derivation data. The recommended
- name of the derivation file has the format <name> ``-deriv.fif`` .
+ name of the derivation file has the format <*name*> ``-deriv.fif`` .
-**\---list <name>**
+**\---list <*name*>**
List the contents of a derivation file to standard output. If this
option is missing and ``--out`` is specified, the content
@@ -492,9 +492,9 @@ All lines in the input files starting with the pound sign
(#) are considered to be comments. The format of a derivation in
a arithmetic input file is:
-<name> ``=`` [<INLINE_EQUATION>``*`` ]<INLINE_EQUATION > ``+`` <INLINE_EQUATION>``*`` ]<INLINE_EQUATION >INLINE_EQUATION
+ <*name*> ``=`` [ <*INLINE_EQUATION*>``*`` ] <*INLINE_EQUATION > ``+`` <*INLINE_EQUATION*>``*`` ] <*INLINE_EQUATION >INLINE_EQUATION
-where <name> is the
+where <*name*> is the
name of the derived channel, INLINE_EQUATION are
the names of the channels comprising the derivation, and INLINE_EQUATION are
their weights. Note that spaces are necessary between the items.
@@ -512,8 +512,8 @@ two times ``EEG 002`` .
The format of a matrix derivation file is:
-<nrow> <ncol> <names of the input channels>
-<INLINE_EQUATION> <weights> INLINE_EQUATION
+ <*nrow*> <*ncol*> <*names of the input channels*>
+ <*INLINE_EQUATION*> <*weights*> INLINE_EQUATION
The combination of the two arithmetic examples, above can
be thus represented as:
@@ -586,7 +586,7 @@ The command-line options are:
List the command-line options.
-**\---lout <name>**
+**\---lout <*name*>**
Specifies the name of the layout file to be output.
@@ -595,16 +595,16 @@ The command-line options are:
Do not fit a sphere to the electrode locations but use a standard sphere
center (INLINE_EQUATION, and INLINE_EQUATION instead.
-**\---prad <value>**
+**\---prad <*value*>**
Specifies a non-standard projection radius INLINE_EQUATION,
see above.
-**\---width <value>**
+**\---width <*value*>**
Specifies the width of the viewports. Default value = 5.
-**\---height <value>**
+**\---height <*value*>**
Specifies the height of the viewports. Default value = 4.
@@ -646,19 +646,19 @@ the following command-line options:
Provide verbose output during the calculations.
-**\---dist <dist/mm>**
+**\---dist <*dist/mm*>**
Invokes the calculation of distances between vertices included in
the source space along the cortical surface. Only pairs whose distance in
the three-dimensional volume is less than the specified distance are
considered. For details, see :ref:`CJAIFJDD`, below.
-**\---src <name>**
+**\---src <*name*>**
The input source space file. The source space files usually end
with ``-src.fif`` .
-**\---srcp <name>**
+**\---srcp <*name*>**
The output source space file which will contain the patch information.
If the file exists it will overwritten without asking for permission.
@@ -667,14 +667,14 @@ the following command-line options:
file is ``mh-7-src.fif`` , a recommended output file name
is ``mh-7p-src.fif`` .
-**\---w <name>**
+**\---w <*name*>**
Name of a w file, which will contain the patch area information. Two
- files will be created: <name> ``-lh.w`` and <name> ``-rh.w`` .
+ files will be created: <*name*> ``-lh.w`` and <*name*> ``-rh.w`` .
The numbers in the files are patch areas in INLINE_EQUATION.
The source space vertices are marked with value 150.
-**\---labeldir <directory>**
+**\---labeldir <*directory*>**
Create a label file corresponding to each of the patches in the
given directory. The directory must be created before running mne_add_patch_info .
@@ -737,22 +737,22 @@ following command-line options:
List the command-line options.
-**\---cov <name>**
+**\---cov <*name*>**
The covariance matrix file to be used a source. The covariance matrix
files usually end with ``-cov.fif`` .
-**\---proj <name>**
+**\---proj <*name*>**
The output file to contain the projection. It is recommended that
the file name ends with ``-proj.fif`` .
-**\---bad <name>**
+**\---bad <*name*>**
Specify channels not to be included when an eigenvalue decomposition
of the covariance matrix is computed.
-**\---include <val1> [:<val2> ]**
+**\---include <*val1*> [: <*val2*> ]**
Select an eigenvector or a range of eigenvectors to include. It
is recommended that magnetometers, gradiometers, and EEG data are handled
@@ -806,11 +806,11 @@ the following command-line options:
List the command-line options.
-**\---bem <name>**
+**\---bem <*name*>**
A BEM file to use. The names of these files usually end with ``bem.fif`` or ``bem-sol.fif`` .
-**\---surf <name>**
+**\---surf <*name*>**
A FreeSurfer surface file to read. This is an alternative to using
a surface from the BEM file.
@@ -821,7 +821,7 @@ the following command-line options:
fitting. If the surface is specified with the ``--surf`` option,
this one is irrelevant.
-**\---mritrans <name>**
+**\---mritrans <*name*>**
A file containing a transformation matrix between the MEG head coordinates
and MRI coordinates. With this option, the sphere origin will be
@@ -854,12 +854,12 @@ the following command-line options:
List the command-line options.
-**\---fwd <name>**
+**\---fwd <*name*>**
Specifies a forward solution file to analyze. By default the MEG
forward solution is considered.
-**\---proj <name>**
+**\---proj <*name*>**
Specifies a file containing an SSP operator to be applied. If necessary,
multiple ``--proj`` options can be specified. For map types 1 - 4 (see
@@ -879,18 +879,18 @@ the following command-line options:
Include MEG magnetometers instead of gradiometers
-**\---w <name>**
+**\---w <*name*>**
Specifies the stem of the output w files. To obtain the final output file
names, ``-lh.w`` and ``-rh.w`` is appended for
the left and right hemisphere, respectively.
-**\---smooth <number>**
+**\---smooth <*number*>**
Specifies the number of smooth steps to apply to the resulting w files.
Default: no smoothing.
-**\---map <number>**
+**\---map <*number*>**
Select the type of a sensitivity map to compute. At present, valid numbers
are 1 - 6. For details, see :ref:`CHDCDJIJ`, below.
@@ -994,26 +994,26 @@ the following command-line options:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies the input file. The file must contain three numbers on
each line which are the *x*, *y*,
and *z* coordinates of point in space. By default,
the input is in millimeters.
-**\---iso <name>**
+**\---iso <*name*>**
Specifies a name of a fif file containing Isotrak data. If this
option is present file will be used as the input instead of the
text file specified with the ``--in`` option.
-**\---trans <name>**
+**\---trans <*name*>**
Specifies the name of a fif file containing the coordinate transformation
between the MEG head coordinates and MRI coordinates. If this file
is not present, the transformation will be replaced by a unit transform.
-**\---out <name>**
+**\---out <*name*>**
Specifies the output file. This file has the same format as the
input file.
@@ -1052,21 +1052,21 @@ The command-line options are:
List the command-line options.
-**\---in <name>**
+**\---in <*name*>**
Specifies the input data file.
-**\---set <number>**
+**\---set <*number*>**
The data set number to compute baselines from or to apply baselines
to. If this option is omitted, all average data sets in the input file
are processed.
-**\---out <name>**
+**\---out <*name*>**
The output file.
-**\---baselines <name>**
+**\---baselines <*name*>**
Specifies a text file which contains the baseline values to be applied. Each
line should contain a channel name, colon, and the baseline value
@@ -1074,19 +1074,19 @@ The command-line options are:
option is encountered, the limits specified by previous ``--bmin`` and ``--bmax`` options will not
have an effect.
-**\---list <name>**
+**\---list <*name*>**
Specifies a text file to contain the baseline values. Listing is
provided only if a specific data set is selected with the ``--set`` option.
-**\---bmin <value/ms>**
+**\---bmin <*value/ms*>**
Lower limit of the baseline. Effective only if ``--baselines`` option is
not present. Both ``--bmin`` and ``--bmax`` must
be present to compute the baseline values. If either ``--bmin`` or ``--bmax`` is
encountered, previous ``--baselines`` option will be ignored.
-**\---bmax <value/ms>**
+**\---bmax <*value/ms*>**
Upper limit of the baseline.
@@ -1118,11 +1118,11 @@ command-line options:
List the command-line options.
-**\---fwd <name>**
+**\---fwd <*name*>**
Specify a forward solution file to employ in the simulation.
-**\---label <name>**
+**\---label <*name*>**
Specify a label
@@ -1134,7 +1134,7 @@ command-line options:
Provide EEG data in the output file.
-**\---out <name>**
+**\---out <*name*>**
Specify the output file. By default, this will be an evoked data
file in the fif format.
@@ -1148,13 +1148,13 @@ command-line options:
Produce Matlab output of the simulated fields instead of the fif evoked
file.
-**\---label <name>**
+**\---label <*name*>**
Define an ROI. Several label files can be present. By default, the sources
in the labels will have INLINE_EQUATION-shaped non-overlapping
timecourses, see below.
-**\---timecourse <name>**
+**\---timecourse <*name*>**
Specifies a text file which contains an expression for a source
time course, see :ref:`CHDCFIBH`. If no --timecourse options
@@ -1164,22 +1164,22 @@ command-line options:
number of expressions is smaller than the number of labels, the
last expression specified will reused for the remaining labels.
-**\---sfreq <freq/Hz>**
+**\---sfreq <*freq/Hz*>**
Specifies the sampling frequency of the output data (default = 1000 Hz). This
option is used only with the time course files.
-**\---tmin <time/ms>**
+**\---tmin <*time/ms*>**
Specifies the starting time of the data, used only with time course files
(default -200 ms).
-**\---tmax <time/ms>**
+**\---tmax <*time/ms*>**
Specifies the ending time of the data, used only with time course files
(default 500 ms).
-**\---seed <number>**
+**\---seed <*number*>**
Specifies the seed for random numbers. This seed is used both for adding
noise, see :ref:`CHDFBJIJ` and for random numbers in source waveform
@@ -1246,7 +1246,7 @@ The ``--timecourse`` option provides flexible possibilities
to define the source waveforms in a functional form. The source
waveform expression files consist of lines of the form:
-<variable> ``=`` <arithmetic expression>
+ <*variable*> ``=`` <*arithmetic expression*>
Each file may contain multiple lines. At the end of the evaluation,
only the values in the variable ``y`` (``q`` )
@@ -1276,7 +1276,7 @@ The available variables are listed in :ref:`CHDJBIEE`.
The arithmetic expressions can use usual arithmetic operations
as well as mathematical functions listed in :ref:`CHDJIBHA`.
The arguments can be vectors or scalar numbers. In addition, standard
-relational operators (<, >, ==, <=, >=) and their textual
+relational operators ( <*, >, ==, <*=, >=) and their textual
equivalents (lt, gt, eq, le, ge) are available. Table :ref:`CHDDJEHH` gives some useful examples of source waveform
expressions.
@@ -1326,7 +1326,7 @@ expressions.
q = 20e-9*sin(2*pi*10*x) A 10-Hz sine wave with 20 nAm amplitude
q = 20e-9*sin(2*pi*2*x)*sin(2*pi*10*x) A 10-Hz 20-nAm sine wave, amplitude modulated sinusoidally at 2 Hz.
q = 20e-9*cosw(t,100,100,100) INLINE_EQUATION-shaped pulse, centered at INLINE_EQUATION with 100 ms leading and trailing slopes, 20 nAm amplitude.
- q = 30e-9*(t > 0)*(t < 300)*sin(2*pi*20*x) 20-Hz sine wave, 30 nAm amplitude, cropped in time to 0...300 ms.
+ q = 30e-9*(t > 0)*(t <* 300)*sin(2*pi*20*x) 20-Hz sine wave, 30 nAm amplitude, cropped in time to 0...300 ms.
============================================= =======================================================================================================================
.. _CHDEDHCG:
@@ -1349,14 +1349,14 @@ The command line options for mne_annot2labels are:
List the command-line options.
-**\---subject <name>**
+**\---subject <*name*>**
Specifies the name of the subject. If this option is not present
the ``$SUBJECT`` environment variable is consulted. If
the subject name cannot be determined, the program quits.
-**\---parc <name>**
+**\---parc <*name*>**
Specifies the parcellation name to convert. The corresponding parcellation
- file names will be ``$SUBJECTS_DIR/$SUBJECT/label/`` <hemi> ``h.`` <name> ``.annot`` where <hemi> is ``l`` or ``r`` for the
+ file names will be ``$SUBJECTS_DIR/$SUBJECT/label/`` <*hemi*> ``h.`` <*name*> ``.annot`` where <*hemi*> is ``l`` or ``r`` for the
left and right hemisphere, respectively.
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git
More information about the debian-med-commit
mailing list