[med-svn] [python-mne] 150/376: fixing manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:24 UTC 2015
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yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 604586b22f5ce5149ea348b17996e6336dfc5b25
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Fri Mar 18 14:14:11 2011 -0400
fixing manual
---
doc/source/manual/analyze.rst | 4 ++--
doc/source/manual/convert.rst | 6 +++---
doc/source/manual/list.rst | 4 ++--
doc/source/manual/mne.rst | 2 +-
doc/source/manual/sampledata.rst | 4 ++--
doc/source/manual/utilities.rst | 12 ++++++------
6 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index c57d5b9..fcd1148 100644
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -528,7 +528,7 @@ The epoch selector contains the following controls:
- The event source specifier. The event source can be either
the data file, *i.e.,* the digital trigger channel or
a event data file produced with mne_browse_raw or mne_process_raw ,
- see Section 4.4.10. Using an event data file is useful
+ see :ref:`CACJGIFA`. Using an event data file is useful
if, *e.g.*, the epochs to be processed epileptic spikes.
- The time range specification. This determines the length of
@@ -568,7 +568,7 @@ which brings up a window with a list of available layouts. The system-wide
layouts reside in $MNE_ROOT/share/mne_analyze/lout. In addition
any layout files residing in $HOME/.mne/lout are listed. The format
of the layout files and selection of the default layout is discussed
-in Section 4.5.6.
+in :ref:`CACFGGCF`.
Several actions can be performed with the mouse in the topographical data
display:
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
index b946733..47bd8f9 100644
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -713,13 +713,13 @@ the EDF/EDF+/BDF file is converted to the fif format in MNE:
- The trigger channel name in BDF files is "Status".
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 Section 4.2.1.
+ invoked, see :ref:`BABBGJEA`.
- Only the two least significant bytes on the "Status" channel
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 Section 4.2.1.
+ see :ref:`BABBGJEA`.
.. _BEHDGAIJ:
@@ -1906,7 +1906,7 @@ the following command-line options are:
The file containing the event definitions. This can be a text or
fif format file produced by mne_process_raw or mne_browse_raw ,
- see Section 4.10.5. With help of this file it is possible
+ see :ref:`CACBCEGC`. With help of this file it is possible
to select virtually any data segment from the raw data file. If
this option is missing, the digital trigger channel in the raw data
file or a fif format event file produced automatically by mne_process_raw or mne_browse_raw is
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index c14db82..ed55bef 100644
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -429,10 +429,10 @@ listed in :ref:`CIHDGFAA`.
| SUBJECT | Name of the current subject. |
+-------------------------+--------------------------------------------+
| MNE_TRIGGER_CH_NAME | Name of the trigger channel in raw data, |
- | | see Section 4.2.1. |
+ | | see :ref:`BABBGJEA`. |
+-------------------------+--------------------------------------------+
| MNE_TRIGGER_CH_MASK | Mask to be applied to the trigger channel |
- | | values, see Section 4.2.1. |
+ | | values, see :ref:`BABBGJEA`. |
+-------------------------+--------------------------------------------+
.. note:: Appendix B contains information specific to the setup at the Martinos Center including instructions to access the Neuromag software.
diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst
index c3307c7..0f7a7f4 100644
--- a/doc/source/manual/mne.rst
+++ b/doc/source/manual/mne.rst
@@ -610,7 +610,7 @@ The command-line options of ``mne_inverse_operator`` are:
**\---proj <name>**
Include signal-space projection (SSP) information from this file. For information
- on SSP, see Section 4.16. If the projections are present in
+ on SSP, see :ref:`CACCHABI`. If the projections are present in
the noise-covariance matrix, the ``--proj`` option is
not allowed.
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index 3be8145..6507503 100644
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -301,7 +301,7 @@ Off-line averaging
##################
Go to directory ``$SAMPLE/MEG/sample`` . With help
-of Section 4.13, familiarize yourself with the averaging
+of :ref:`CACBBDGC`, familiarize yourself with the averaging
script ``audvis.ave`` .
Using the averaging script interactively
@@ -479,7 +479,7 @@ In this case the projections are set on. The projection information
is then attached to the noise-covariance matrix and will be automatically
loaded when the inverse-operator decomposition is computed.
-.. note:: You can study the contents of the covariance matrix computation description file ``audvis.cov`` with help of Section 4.14
+.. note:: You can study the contents of the covariance matrix computation description file ``audvis.cov`` with the help of :ref:`CACEBACG`.
.. _CHDIJBIG:
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
index 43b2de5..fc95d9a 100644
--- a/doc/source/manual/utilities.rst
+++ b/doc/source/manual/utilities.rst
@@ -276,7 +276,7 @@ to this channel. The channel type options are listed in :ref:`CHDFHGCA`.
.. warning:: Do not attempt to designate MEG channels to EEG channels or vice versa. This may result in strange errors during source estimation.
-.. note:: You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system. This allows you to use standard EEG channel names when defining derivations, see Sections :ref:`CHDHJABJ` and 4.4.12, as well as in the channel selection files used in mne_browse_raw , see Section 4.5.5.
+.. note:: You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system. This allows you to use standard EEG channel names when defining derivations, see :ref:`CHDHJABJ` and :ref:`CACFHAFH`, as well as in the channel selection files used in mne_browse_raw , see :ref:`CACCJEJD`.
.. _CHDBDDDF:
@@ -533,9 +533,9 @@ the following criteria have to be met:
in the currently loaded data set.
The validity check is done when a derivation file is loaded
-into mne_browse_raw , see Section 4.4.12.
+into mne_browse_raw , see :ref:`CACFHAFH`.
-.. note:: You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system using the mne_rename_channels utility, see :ref:`CHDCFEAJ`. This allows you to use standard EEG channel names in the derivations you define as well as in the channel selection files used in mne_browse_raw , see Section 4.5.5.
+.. note:: You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system using the mne_rename_channels utility, see :ref:`CHDCFEAJ`. This allows you to use standard EEG channel names in the derivations you define as well as in the channel selection files used in mne_browse_raw , see :ref:`CACCJEJD`.
.. _CHDDGDJA:
@@ -545,8 +545,8 @@ Creating a custom EEG layout
Purpose
=======
-Both MNE software (mne_analyze and mne_browse_raw )
-and Neuromag software (xplotter and xfit )
+Both MNE software (mne_analyze and mne_browse_raw)
+and Neuromag software (xplotter and xfit)
employ text layout files to create topographical displays of MEG
and EEG data. While the MEG channel layout is fixed, the EEG layout
varies from experiment to experiment, depending on the number of
@@ -925,7 +925,7 @@ Furthermore, assume that the colums orthogonal matrix INLINE_EQUATION (INLINE_EQ
the orthogonal basis of the noise subspace corresponding to the signal
space projection (SSP) operator INLINE_EQUATION specified
with one or more ``--proj`` options so that INLINE_EQUATION.
-For more information on SSP, see Section 4.16.
+For more information on SSP, see :ref:`CACCHABI`.
With these definitions the map selections defined with the ``--map`` option correspond
to the following
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