[med-svn] [python-mne] 188/376: fixing manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:34 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 850d2dabf90a9ad1d384ec5dae7dbff9355927e5
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Mon Apr 11 10:32:23 2011 -0400
fixing manual
---
doc/source/manual/AppA.rst | 10 +++---
doc/source/manual/AppReleaseNotes.rst | 42 ++++++++++++------------
doc/source/manual/analyze.rst | 8 ++---
doc/source/manual/browse.rst | 8 ++---
doc/source/manual/convert.rst | 62 ++++++++++++++++++++++-------------
doc/source/manual/cookbook.rst | 8 ++---
doc/source/manual/forward.rst | 12 +++----
doc/source/manual/list.rst | 2 +-
doc/source/manual/matlab.rst | 2 +-
doc/source/manual/mne.rst | 10 +++---
doc/source/manual/sampledata.rst | 2 +-
doc/source/manual/utilities.rst | 24 +++++++-------
12 files changed, 103 insertions(+), 87 deletions(-)
diff --git a/doc/source/manual/AppA.rst b/doc/source/manual/AppA.rst
index b730f3d..5abd27a 100755
--- a/doc/source/manual/AppA.rst
+++ b/doc/source/manual/AppA.rst
@@ -162,7 +162,7 @@ already in place. The following options can be specified:
**\---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
@@ -185,7 +185,7 @@ the following:
- Set the ``SUBJECTS_DIR`` and ``SUBJECT`` environment
variables
-.. note:: If mne_flash_bem is run with the --noflash30 option, the flash30 directory is not needed, *i.e.*, only the 5-degree flip angle flash data are employed.
+.. note:: If mne_flash_bem is run with the ``--noflash30`` option, the flash30 directory is not needed, *i.e.*, only the 5-degree flip angle flash data are employed.
It may take a while for mne_flash_bem to
complete. It uses the FreeSurfer directory structure under ``$SUBJECTS_DIR/$SUBJECT`` .
@@ -195,7 +195,7 @@ The script encapsulates the following processing steps:
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`` .
-- If the --unwarp option is specified, run grad_unwarp and produce
+- If the ``--unwarp`` option is specified, run grad_unwarp and produce
files ``mef`` <flip-angle> _<echo-number> ``u.mgz`` .
These files will be then used in the following steps.
@@ -223,7 +223,7 @@ The script encapsulates the following processing steps:
- The COR format volumes created by mne_flash_bem are
removed.
-If the --noflash30 option is specified to mne_flash_bem ,
+If the ``--noflash30`` option is specified to mne_flash_bem ,
steps 3 and 4 in the above are replaced by averaging over the different
echo times in 5-degree flip angle data.
@@ -372,6 +372,6 @@ is:
Proceed to mne_setup_forward_model .
Use the ``--surf`` and ``--noswap`` options.
-.. note:: If left and right are flipped in BrainSuite, use the --flip option in mne_convert_surface to set the coordinate transformation correctly.
+.. note:: If left and right are flipped in BrainSuite, use the ``--flip`` option in mne_convert_surface to set the coordinate transformation correctly.
.. note:: The BrainSuite scalp surface can be also used for visualization in mne_analyze , see :ref:`CHDCGHIF`.
diff --git a/doc/source/manual/AppReleaseNotes.rst b/doc/source/manual/AppReleaseNotes.rst
index eb76545..9aae983 100755
--- a/doc/source/manual/AppReleaseNotes.rst
+++ b/doc/source/manual/AppReleaseNotes.rst
@@ -484,7 +484,7 @@ Improvements in the raw data processor mne_browse_raw /mne_process_raw include:
- Added possibility to compute a projection operator from epochs
specified by events.
-- Added the keepsamplemean option
+- Added the ``--keepsamplemean`` option
to the covariance matrix computation files.
- Added the ``--digtrigmask`` option.
@@ -550,7 +550,7 @@ the dipole position coordinates, see :ref:`CHDDIBAH`.
mne_list_bem
------------
-The --surfno option is replaced with the --id option, see :ref:`BEHBBEHJ`.
+The ``--surfno`` option is replaced with the ``--id`` option, see :ref:`BEHBBEHJ`.
mne_make_cor_set
----------------
@@ -562,8 +562,8 @@ the output file if possible. For details, see :ref:`BABBHHHE`.
mne_make_movie
--------------
-Added the --noscalebar, --nocomments, --morphgrade, --rate,
-and --pickrange options, see :ref:`CBBECEDE`.
+Added the ``--noscalebar``, ``--nocomments``, ``--morphgrade``, ``--rate``,
+and ``--pickrange`` options, see :ref:`CBBECEDE`.
mne_make_source_space
---------------------
@@ -737,9 +737,9 @@ mne_browse_raw
- Possibility to detect temporal skew between trigger input
lines has been added, see :ref:`BABIHFBI` and :ref:`BABCGEJE`.
-- --allowmaxshield option now works in the batch mode as well.
+- ``--allowmaxshield`` option now works in the batch mode as well.
-- Added the --projevent option to batch mode.
+- Added the ``--projevent`` option to batch mode.
- It is now possible to compute an SSP operator for EEG, see :ref:`CACEAHEI`.
@@ -765,31 +765,31 @@ Miscellaneous
and bin/admin directories.
- mne_anonymize now has the
- --his option to remove the HIS ID of the subject, see :ref:`CHDIJHIC`.
+ ``--his`` option to remove the HIS ID of the subject, see :ref:`CHDIJHIC`.
- mne_check_surface now has
- the --bem and --id options to check surfaces from a BEM fif file.
+ the ``--bem`` and ``--id`` options to check surfaces from a BEM fif file.
For details, try mne_check_surface --help.
- mne_compute_raw_inverse now
- has the --orignames option, see :ref:`CHDEIHFA`.
+ has the ``--orignames`` option, see :ref:`CHDEIHFA`.
-- Added --headcoord option to mne_convert_dig_data ,
+- Added ``--headcoord`` option to mne_convert_dig_data ,
see :ref:BABCJEAD`.
-- Added --talairach option to mne_make_cor_set ,
+- Added ``--talairach`` option to mne_make_cor_set ,
see :ref:`BABBHHHE`.
-- Added the --morph option to mne_setup_source_space and mne_make_source_space ,
+- Added the ``--morph`` option to mne_setup_source_space and mne_make_source_space ,
see :ref:`CIHCHDAE` and :ref:`BEHCGJDD`, respectively.
-- Added the --prefix option to mne_morph_labels ,
+- Added the ``--prefix`` option to mne_morph_labels ,
see :ref:`CHDCEAFC`.
-- Added the --blocks and --indent options to mne_show_fiff ,
+- Added the ``--blocks`` and ``--indent`` options to mne_show_fiff ,
see :ref:`CHDHEDEF`.
-- Added the --proj option as well as map types 5 and 6 to mne_sensitivity_map ,
+- Added the ``--proj`` option as well as map types 5 and 6 to mne_sensitivity_map ,
see :ref:`CHDDCBGI`.
- Fixed a bug in mne_inverse_operator which
@@ -839,13 +839,13 @@ Matlab toolbox
Miscellaneous
=============
-- Added --shift option to mne_convert_surface ,
+- Added ``--shift`` option to mne_convert_surface ,
see :ref:`BABEABAA`.
-- Added --alpha option to mne_make_movie ,
+- Added ``--alpha`` option to mne_make_movie ,
see :ref:`CBBBBHIF`.
-- Added --noiserank option to mne_inverse_operator and mne_do_inverse_operator ,
+- Added ``--noiserank`` option to mne_inverse_operator and mne_do_inverse_operator ,
see :ref:`CBBDDBGF`and :ref:`CIHCFJEI`, respectively.
- The fif output from mne_convert_dig_data now
@@ -853,7 +853,7 @@ Miscellaneous
systems if such a transformation has been requested, see :ref:`BABCJEAD`.
This also affects the output from mne_eximia2fiff, see :ref:`BEHGCEHH`.
-- Added --noflash30, --noconvert, and --unwarp options to mne_flash_bem ,
+- Added ``--noflash30``, ``--noconvert``, and ``--unwarp`` options to mne_flash_bem ,
see :ref:`BABFCDJH`.
Release notes for MNE software 2.7.3
@@ -865,11 +865,11 @@ Miscellaneous
- Added preservation of the volume geometry
information in the FreeSurfer surface files.
-- The --mghmri option in combination with --surfout inserts
+- The ``--mghmri`` option in combination with ``--surfout`` inserts
the volume geometry information to the output of mne_convert_surface ,
see :ref:`BEHDIAJG`.
-- Added --replacegeom option to mne_convert_surface ,
+- Added ``--replacegeom`` option to mne_convert_surface ,
see :ref:`BEHDIAJG`.
- Modified mne_watershed_bem and mne_flash_bem to
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index 98c171b..f55d578 100755
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -110,7 +110,7 @@ options:
Specify a file containing the transformation between the MEG device
and head coordinate frames. This option is only usable if the *head
position visualization* position visualization mode has
- been first invoked with the --visualizehpi option.
+ been first invoked with the ``--visualizehpi`` option.
**\---scalehead**
@@ -2682,7 +2682,7 @@ Visualizing the head position
#############################
When mne_analyze is invoked
-with the --visualizehpi option, a simplified user interface shown
+with the ``--visualizehpi`` option, a simplified user interface shown
in :ref:`CHDJJGII` is displayed. This interface consists only
of the viewer window. This *head position visualization* mode
can be used with existing data files but is most useful for showing
@@ -2717,7 +2717,7 @@ place:
between the MEG device and head coordinate frames, as well as the
average head surface provided with the MNE software are loaded.
-- If the --scalehead option is invoked, the average head surface
+- If the ``--scalehead`` option is invoked, the average head surface
is scaled to the approximate size of the subject's head
by fitting a sphere to the digitizer and to the head surface points
lying above the plane of the fiducial landmarks, respectively. The
@@ -2738,7 +2738,7 @@ place:
HPI, the position of the MEG helmet surface is shown in the viewer
window.
-If the --rthelmet option was present, the room-temperature
+If the ``--rthelmet`` option was present, the room-temperature
helmet surface is shown instead of the MEG sensor surface. The digitizer
and HPI data files are reloaded and the above steps 1. - 4. are
repeated when the Reload HPI button
diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst
index 2eee0df..31d1b50 100755
--- a/doc/source/manual/browse.rst
+++ b/doc/source/manual/browse.rst
@@ -31,8 +31,8 @@ Command-line options
####################
This section first describes the options common to mne_browse_raw and mne_process_raw .
-Thereafter, options unique to the interactive (mne_browse_raw )
-and batch (mne_process_raw ) modes are
+Thereafter, options unique to the interactive (mne_browse_raw)
+and batch (mne_process_raw) modes are
listed.
.. _BABBGJEA:
@@ -176,7 +176,7 @@ Common options
Interactive mode options
========================
-These options apply to the interactive (mne_browse_raw )
+These options apply to the interactive (mne_browse_raw)
version only.
**\---allowmaxshield**
@@ -2523,7 +2523,7 @@ 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.
-If the recommended keepsamplemean option
+If the recommended ``--keepsamplemean`` option
is specified in the covariance matrix definition file, the baseline
correction is applied to the epochs but the means at individual
samples are not subtracted. Thus the covariance matrix will be computed
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
index 0557940..95f0cc5 100755
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -246,7 +246,7 @@ sensor channels, INLINE_EQUATION reference sensor
channels, and INLINE_EQUATION other channels.
The data from all channels can be concatenated into a single vector
-.. math:: 1 + 1 = 2
+.. math:: x = [x_1^T x_2^T x_3^T]^T\ ,
where INLINE_EQUATION, INLINE_EQUATION,
and INLINE_EQUATION are the data vectors corresponding
@@ -255,23 +255,31 @@ channels, respectively. The data before and after compensation,
denoted here by INLINE_EQUATION and INLINE_EQUATION, respectively,
are related by
-.. math:: 1 + 1 = 2
+.. math:: x_{(k)} = M_{(k)} x_{(0)}\ ,
where the composite compensation matrix is
-.. math:: 1 + 1 = 2
+.. math:: M_{(k)} = \begin{bmatrix}
+ I_{n_1} & C_{(k)} & 0 \\
+ 0 & I_{n_2} & 0 \\
+ 0 & 0 & I_{n_3}
+ \end{bmatrix}\ .
In the above, INLINE_EQUATION is a INLINE_EQUATION compensation
data matrix corresponding to compensation "grade" INLINE_EQUATION.
It is easy to see that
-.. math:: 1 + 1 = 2
+.. math:: M_{(k)}^{-1} = \begin{bmatrix}
+ I_{n_1} & -C_{(k)} & 0 \\
+ 0 & I_{n_2} & 0 \\
+ 0 & 0 & I_{n_3}
+ \end{bmatrix}\ .
To convert from compensation grade INLINE_EQUATION to INLINE_EQUATION one
can simply multiply the inverse of one compensate compensation matrix
by another and apply the product to the data:
-.. math:: 1 + 1 = 2
+.. math:: x_{(k)} = M_{(k)} M_{(p)}^{-1} x_{(p)}\ .
This operation is performed by mne_compensate_data ,
which has the following command-line options:
@@ -473,12 +481,15 @@ trigger channel data, see the ``--stim`` option, below.
The synthesized trigger channel data value at sample INLINE_EQUATION will
be:
-.. math:: 1 + 1 = 2
+.. math:: s(k) = \sum_{p = 1}^n {t_p(k) 2^{p - 1}}\ ,
where INLINE_EQUATION are the thresholded
from the input channel data INLINE_EQUATION:
-.. math:: 1 + 1 = 2
+.. math:: t_p(k) = \Bigg\{ \begin{array}{l}
+ 0 \text{ if } d_p(k) \leq t\\
+ 1 \text{ if } d_p(k) > t
+ \end{array}\ .
The threshold value INLINE_EQUATION can
be adjusted with the ``--stimthresh`` option, see below.
@@ -612,7 +623,7 @@ be used to store trigger information. The Time-stamped Annotation
Lists (TALs) on the annotation data can be converted to a trigger
channel (STI 014) using an annotation map file which associates
an annotation label with a number on the trigger channel. The TALs
-can be listed with the --listtal option,
+can be listed with the ``--listtal`` option,
see below.
.. warning:: The data samples in a BDF file are represented in a 3-byte (24-bit) format. Since 3-byte raw data buffers are not presently supported in the fif format these data will be changed to 4-byte integers in the conversion. Since the maximum size of a fif file is 2 GBytes, the maximum size of a BDF file to be converted is approximately 1.5 GBytes
@@ -640,12 +651,12 @@ The command-line options of mne_edf2fiff are:
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,
- see the --annotmap option, below.
+ see the ``--annotmap`` option, below.
This output file is an event file compatible with mne_browse_raw and mne_process_raw ,
see :ref:`ch_browse`. In addition, in the mapping between TAL
- labels and trigger numbers provided by the --annotmap option is
+ labels and trigger numbers provided by the ``--annotmap`` option is
employed to assign trigger numbers in the event file produced. In
- the absense of the --annotmap option default trigger number 1024
+ the absense of the ``--annotmap`` option default trigger number 1024
is used.
**\---annotmap <filename>**
@@ -711,12 +722,12 @@ the EDF/EDF+/BDF file is converted to the fif format in MNE:
see :ref:`CHDDGDJA`.
- The trigger channel name in BDF files is "Status".
- This must be specified with the --digtrig option or with help of
+ This must be specified with the ``--digtrig`` option or with help of
the MNE_TRIGGER_CH_NAME environment variable when mne_browse_raw or mne_process_raw is
invoked, see :ref:`BABBGJEA`.
- Only the two least significant bytes on the "Status" channel
- of BDF files are significant as trigger information the --digtrigmask
+ of BDF files are significant as trigger information the ``--digtrigmask``
0xff option MNE_TRIGGER_CH_MASK environment variable should be used
to specify this to mne_browse_raw and mne_process_raw ,
see :ref:`BABBGJEA`.
@@ -854,7 +865,7 @@ to the fif format with help of the mne_eximia2fiff script.
It creates a BrainVision ``vhdr`` file and calls mne_brain_vision2fiff.
Usage:
-``mne_eximia2fiff`` [--dig dfile ] [``--orignames`` ] file1 file2 ...
+``mne_eximia2fiff`` [``--dig`` dfile ] [``--orignames`` ] file1 file2 ...
where file1 file2 ...
are eXimia ``nxe`` files and the ``--orignames`` option
@@ -863,7 +874,7 @@ If you want to convert all data files in a directory, say
``mne_eximia2fiff *.nxe``
-The optional file specified with the --dig option is assumed
+The optional file specified with the ``--dig`` option is assumed
to contain digitizer data from the recording in the Nexstim format.
The resulting fif data file will contain these data converted to
the fif format as well as the coordinate transformation between
@@ -982,7 +993,7 @@ where
Location of the point, usually in the MEG head coordinate system, see :ref:`BJEBIBAI`.
Some programs have options to accept coordinates in meters instead
- of millimeters. With --meters option, mne_transform_points lists
+ of millimeters. With ``--meters`` option, mne_transform_points lists
the coordinates in meters.
.. _BEHDEJEC:
@@ -1182,7 +1193,7 @@ Converting surface data between different formats
The utility mne_convert_surface converts
surface data files between different formats.
-.. note:: The MNE Matlab toolbox functions enable reading of FreeSurfer surface files directly. Therefore, the --mat option has been removed. The dfs file format conversion functionality has been moved here from mne_convert_dfs . Consequently, mne_convert_dfs has been removed from MNE software.
+.. note:: The MNE Matlab toolbox functions enable reading of FreeSurfer surface files directly. Therefore, the ``--mat`` option has been removed. The dfs file format conversion functionality has been moved here from mne_convert_dfs . Consequently, mne_convert_dfs has been removed from MNE software.
.. _BABEABAA:
@@ -1245,7 +1256,7 @@ the following command-line options:
coordinates, *i.e.*, the coordinate system of
the MRI stack in the file. In addition, this option can be used
to insert "volume geometry" information to the FreeSurfer
- surface file output (--surfout option). If the input file already
+ surface file output (``--surfout`` option). If the input file already
contains the volume geometry information, --replacegeom is needed
to override the input volume geometry and to proceed to writing
the data.
@@ -1253,7 +1264,7 @@ the following command-line options:
**\---replacegeom**
Replaces existing volume geometry information. Used in conjunction
- with the --mghmri option described above.
+ with the ``--mghmri`` option described above.
**\---fifmri <name>**
@@ -1321,13 +1332,18 @@ the following command-line options:
The coordinate transformation file specified with the ``--trans`` should contain
a 4 x 4 coordinate transformation matrix:
-.. math:: 1 + 1 = 2
+.. math:: T = \begin{bmatrix}
+ R_{11} & R_{12} & R_{13} & x_0 \\
+ R_{13} & R_{13} & R_{13} & y_0 \\
+ R_{13} & R_{13} & R_{13} & z_0 \\
+ 0 & 0 & 0 & 1
+ \end{bmatrix}
defined so that if the augmented location vectors in the
dfs file and MRI coordinate systems are denoted by INLINE_EQUATION and INLINE_EQUATION,
respectively,
-.. math:: 1 + 1 = 2
+.. math:: r_{MRI} = Tr_{dfs}
.. _BABBHHHE:
@@ -1704,7 +1720,7 @@ 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
@@ -2030,7 +2046,7 @@ contains INLINE_EQUATION channels and INLINE_EQUATION time
points, the data INLINE_EQUATION ar e ordered
as
-.. math:: 1 + 1 = 2
+.. math:: s_{111} \dotso s_{1n1} s_{211} \dotso s_{mn1} \dotso s_{mnp}\ ,
where the first index stands for the time point, the second
for the channel, and the third for the epoch number, respectively.
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
index 8164b5a..98b975c 100755
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -30,7 +30,7 @@ Before starting the data analysis, setup the environment
variable SUBJECTS_DIR to select the directory under which the anatomical
MRI data are stored. Optionally, set SUBJECT as the name of the
subject's MRI data directory under SUBJECTS_DIR. With this
-setting you can avoid entering the --subject option common to many
+setting you can avoid entering the ``--subject`` option common to many
MNE programs and scripts. In the following sections, files in the
FreeSurfer directory hierarchy are usually referred to without specifying
the leading directories. Thus, bem/msh-7-src.fif is used to refer
@@ -441,7 +441,7 @@ 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
- the BEM geometry in fif format. The latter file is created if -homog
+ the BEM geometry in fif format. The latter file is created if ``--homog``
option is specified. Here, <ntri-xxx> indicates
the number of triangles on the corresponding surface.
@@ -472,7 +472,7 @@ using Import/Strings from the File menu.
.. note:: With help of the ``--nosol`` option it is possible to create candidate BEM geometry data files quickly and do the checking with respect to the anatomical MRI data. When the result is satisfactory, mne_setup_forward_model can be run without ``--nosol`` to invoke the time-consuming calculation of the solution file as well.
-.. note:: The triangle meshes created by the seglab program have counterclockwise vertex ordering and thus require the --noswap option.
+.. note:: The triangle meshes created by the seglab program have counterclockwise vertex ordering and thus require the ``--noswap`` option.
.. note:: Up to this point all processing stages depend on the anatomical (geometrical) information only and thus remain identical across different MEG studies.
@@ -1009,7 +1009,7 @@ the following options:
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
+ <options> includes options ``--meg``, ``--eeg``, and ``--fixed`` with the double
dashes replaced by single ones.
**\---destdir <directory>**
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index 20f7e12..1a2eb93 100755
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -279,7 +279,7 @@ The command-line options are:
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
+ benefit of the ``--ico`` option is that the source space will have triangulation
information between the decimated vertices included, which some
future versions of MNE software may be able to utilize. The number
of triangles increases by a factor of four in each subdivision,
@@ -575,7 +575,7 @@ topology checks are performed:
be very close to INLINE_EQUATION. If the result
is INLINE_EQUATION instead, it is conceivable
that the ordering of the triangle vertices is incorrect and the
- --swap option should be specified.
+ ``--swap`` option should be specified.
- The correct ordering of the surfaces is verified by checking
that the surfaces are inside each other as expected. This is accomplished
@@ -1079,7 +1079,7 @@ the following command-line options:
**\---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
+ from head to mri coordinates. With ``--trans``, ``--mri`` option is not
required.
**\---notrans**
@@ -1209,7 +1209,7 @@ inner skull surface.
Field derivatives
=================
-If the --grad **problem - double dash shows up in html as single long dash..!** option is specified, mne_forward_solution includes
+If the ``--grad`` option is specified, mne_forward_solution includes
the derivatives of the forward solution with respect to the dipole
location coordinates to the output file. Let
@@ -1221,7 +1221,7 @@ up INLINE_EQUATIONthe gain matrix
.. math:: G = [G_1 \dotso G_{N_{source}}]\ .
-With the --grad option, the output from mne_forward_solution also
+With the ``--grad`` option, the output from mne_forward_solution also
contains the INLINE_EQUATION derivative matrix
.. math:: D = [D_1 \dotso D_{N_{source}}]\ ,
@@ -1232,7 +1232,7 @@ where
where INLINE_EQUATION are the location
coordinates of the INLINE_EQUATION dipole. If
-the dipole orientations are to the cortical normal with the --fixed
+the dipole orientations are to the cortical normal with the ``--fixed``
option, the dimensions of INLINE_EQUATION and INLINE_EQUATION are INLINE_EQUATION and INLINE_EQUATION,
respectively. Both INLINE_EQUATION and INLINE_EQUATION can
be read with the mne_read_forward_solution Matlab
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index 45d04c5..f1f093e 100755
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -344,7 +344,7 @@ 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.
-All software modules employ the double-dash (--) option convention, *i.e.*, the
+All software modules employ the double-dash (``--``) option convention, *i.e.*, the
option names are preceded by two dashes.
Most of the programs have two common options to obtain general
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index 822f6f9..cc0c92f 100755
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -641,7 +641,7 @@ The documented structures are:
nearest int32(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the nearest active source space vertex.
nearest_dist double(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the distance to the nearest active source space vertex.
dist double(np,np) Distances between vertices on this surface given as a sparse matrix. A zero off-diagonal entry in this matrix indicates that the corresponding distance has not been calculated.
- dist_limit double The value given to mne_add_patch_info with the --dist option, see :ref:`CJAGCDCC`. This value is presently always negative, indicating that only distances between active source space vertices, as indicated by the vertno field of this structure, have been calculated.
+ dist_limit double The value given to mne_add_patch_info with the ``--dist`` option, see :ref:`CJAGCDCC`. This value is presently always negative, indicating that only distances between active source space vertices, as indicated by the vertno field of this structure, have been calculated.
=============== ================== ============================================================================================================================================================================================================================================================================
.. _BGBJJIED:
diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst
index 64be025..d3637bc 100755
--- a/doc/source/manual/mne.rst
+++ b/doc/source/manual/mne.rst
@@ -477,7 +477,7 @@ The command-line options of ``mne_inverse_operator`` are:
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???**
+ blaa...***what???**
**\---fwd <name>**
@@ -488,12 +488,12 @@ The command-line options of ``mne_inverse_operator`` are:
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.
+ backward compatibility, ``--senscov`` can be used as a synonym for ``--noisecov``.
**\---noiserank <value>**
Specifies the rank of the noise covariance matrix explicitly rather than
- trying to reduce it automatically. This option is sheldom needed,
+ trying to reduce it automatically. This option is seldom needed,
**\---gradreg <value>**
@@ -575,7 +575,7 @@ The command-line options of ``mne_inverse_operator`` are:
**\---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 ``--noise`` cov option
+ line of the file. If the noise-covariance matrix specified with the ``--noisecov`` option
contains projections, bad channel lists can be included only if
they specify all channels containing non-zero entries in a projection
vector. For example, bad channels can usually specify all magnetometers
@@ -838,7 +838,7 @@ Visualization options
of the complete cortical surface. A complete name of a patch file
in the FreeSurface surf directory must be given. The name should
begin with lh or rh to allow association of the patch with a hemisphere.
- Maximum of two --patch options can be in effect, one patch for each
+ Maximum of two ``--patch`` options can be in effect, one patch for each
hemisphere. If the name refers to a flat patch, the name can be
optionally followed by a colon and a rotation angle in degrees.
The flat patch will be then rotated counterclockwise by this amount
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index 1114152..17711e6 100755
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -360,7 +360,7 @@ The functions of the options are:
Specifies how the averages are named. With this option, the ``_raw.fif`` ending
is stripped of the original raw data file and the tag specified
- with this option (``-ave`` ) is added. The average file
+ with this option (``--ave`` ) is added. The average file
and the corresponding log file will have the extensions ``.fif`` and ``.log`` , respectively.
**\---ave**
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
index afbdced..a5f485c 100755
--- a/doc/source/manual/utilities.rst
+++ b/doc/source/manual/utilities.rst
@@ -220,7 +220,7 @@ in MEG/EEG data files. Such situations include:
- Changing the name of the digital trigger channel of interest
to STI 014 so that mne_browse_raw and mne_process_raw will
- recognize the correct channel without the need to specify the --digtrig
+ recognize the correct channel without the need to specify the ``--digtrig``
option or the MNE_TRIGGER_CH_NAME environment variable every time a
data file is loaded.
@@ -358,7 +358,7 @@ file:
FIFF_SUBJ_COMMENT Comment about the subject
======================== ==============================================
-.. note:: mne_anonymize normally keeps the FIFF_SUBJ_HIS_ID tag which can be used to identify the subjects uniquely after the information listed in :ref:`CHDEHBCG` have been removed. If the --his option is specified on the command line, the FIFF_SUBJ_HIS_ID tag will be removed as well. The data of the tags listed in :ref:`CHDEHBCG` and the optional FIFF_SUBJ_HIS_ID tag are overwritten with zeros and the space claimed by omitting these tags is added to the free space [...]
+.. note:: mne_anonymize normally keeps the FIFF_SUBJ_HIS_ID tag which can be used to identify the subjects uniquely after the information listed in :ref:`CHDEHBCG` have been removed. If the ``--his`` option is specified on the command line, the FIFF_SUBJ_HIS_ID tag will be removed as well. The data of the tags listed in :ref:`CHDEHBCG` and the optional FIFF_SUBJ_HIS_ID tag are overwritten with zeros and the space claimed by omitting these tags is added to the free sp [...]
mne_anonymize recognizes
the following command-line options:
@@ -698,16 +698,16 @@ the sizes of the patches, their average normals, and the standard
deviation of the normal directions. This information is also returned
by the mne_read_source_space Matlab function as described in Table 10.28.
-The --dist option to mne_add_patch_info invokes
+The ``--dist`` option to mne_add_patch_info invokes
the calculation of inter-vertex distances. These distances are computed
along the the cortical surface (usually the white matter) on which
the source space vertices are located.
Since the calculation of all possible distances would take
-a very long time, the distance given with the --dist option allows
+a very long time, the distance given with the ``--dist`` option allows
restriction to the neighborhood of each source space vertex. This
neighborhood is defined as the sphere around each source space vertex,
-with radius given by the --dist option. Because the distance calculation
+with radius given by the ``--dist`` option. Because the distance calculation
is done along the folded cortical surface whose details are given
by the dense triangulation of the cortical surface produced by FreeSurfer,
some of the distances computed will be larger than the value give
@@ -862,7 +862,7 @@ the following command-line options:
**\---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
+ multiple ``--proj`` options can be specified. For map types 1 - 4 (see
below), SSP is applied to the forward model data. For map types
5 and 6, the effects of SSP are evaluated against the unmodified
forward model.
@@ -902,7 +902,7 @@ Available sensitivity maps
In the following, let
-.. math:: 1 + 1 = 2
+.. math:: G_k = [g_{xk} g_{yk} g_{zk}]
denote the three consecutive columns of the gain matrix INLINE_EQUATION corresponding to
the fields of three orthogonal dipoles at source space location INLINE_EQUATION.
@@ -912,7 +912,7 @@ to the cortical normal direction and the INLINE_EQUATION plane
is thus the tangent plane of the cortex at the source space location INLINE_EQUATION.
Next, compute the SVD
-.. math:: 1 + 1 = 2
+.. math:: G_k = U_k \Lambda_k V_k
and let INLINE_EQUATION, where INLINE_EQUATION and INLINE_EQUATION are
the largest singular value and the corresponding left singular vector
@@ -1202,12 +1202,12 @@ by first generating vectors of Gaussian random numbers INLINE_EQUATION with INLI
Thereafter, the noise-covariance matrix INLINE_EQUATIONis
used to color the noise:
-.. math:: 1 + 1 = 2
+.. math:: n_c(t) = \frac{1}{\sqrt{L}} \Lambda U^T n(t)\ ,
where we have used the eigenvalue decomposition positive-definite
covariance matrix:
-.. math:: 1 + 1 = 2
+.. math:: C = U \Lambda^2 U^T\ .
Note that it is assumed that the noise-covariance matrix
is given for raw data, *i.e.*, for INLINE_EQUATION.
@@ -1220,7 +1220,7 @@ Simulated data
The default source waveform INLINE_EQUATION for
the INLINE_EQUATION label is nonzero at times INLINE_EQUATION, INLINE_EQUATION with:
-.. math:: 1 + 1 = 2
+.. math:: q_k(t_{kp}) = Q_k \cos^2{(\frac{\pi p}{100} - \frac{\pi}{2})}\ ,
i.e., the source waveforms are non-overlapping 100-samples
wide INLINE_EQUATION pulses. The sampling frequency INLINE_EQUATION.
@@ -1232,7 +1232,7 @@ potentials produced by the dipoles normal to the cortical mantle
at label INLINE_EQUATION **by INLINE_EQUATION. The simulated
signals are then:
-.. math:: 1 + 1 = 2
+.. math:: x(t_j) = \sum_{k = 1}^{N_s} {q_k(t_j) x_k + n_c(t_j)}\ ,
where INLINE_EQUATION is the number of
sources.
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