[med-svn] [python-mne] 147/376: 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 038454fb0211266b4b9970ce05f48ae6e98f07b4
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Thu Mar 17 12:08:01 2011 -0400
fixing manual
---
doc/source/manual/browse.rst | 10 ++++-----
doc/source/manual/convert.rst | 6 +++---
doc/source/manual/list.rst | 46 ++++++++++++++++++++--------------------
doc/source/manual/matlab.rst | 4 ++--
doc/source/manual/mne.rst | 2 +-
doc/source/manual/sampledata.rst | 2 +-
doc/source/manual/utilities.rst | 2 +-
7 files changed, 36 insertions(+), 36 deletions(-)
diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst
index 37dfba4..d23890b 100644
--- a/doc/source/manual/browse.rst
+++ b/doc/source/manual/browse.rst
@@ -588,7 +588,7 @@ Load derivations
This menu choice allows loading of channel derivation data
files created with the mne_make_derivations utility,
-see Section 11.5, or using the interactive derivations
+see :ref:`CHDHJABJ`, or using the interactive derivations
editor in mne_browse_raw , see :ref:`CACJIEHI`, Most common use of derivations is to calculate
differences between EEG channels, *i.e.*, bipolar
EEG data. Since any number of channels can be included in a derivation
@@ -860,7 +860,7 @@ Brings up the interactive derivations editor. This editor
can be used to add or modify derived channels, *i.e.*,
linear combinations of signals actually recorded. Channel derivations
can be also created and modified using the mne_make_derivations tool,
-see Section 11.5. The interactive editor contains two main
+see :ref:`CHDHJABJ`. The interactive editor contains two main
areas:
- Interactive tools for specifying a channel
@@ -886,7 +886,7 @@ associated selections interactively involves the following steps:
- If desired, EEG channels can be relabeled
with descriptive names using the mne_rename_channels utility,
- see Section 11.4.5. It is strongly recommended that you
+ see :ref:`CHDCFEAJ`. It is strongly recommended that you
keep a copy of the channel alias file used by mne_rename_channels .
If necessary, you can then easily return to the original channel
names by running mne_rename_channels again
@@ -1069,7 +1069,7 @@ for the Neuromag Vectorview data because newer systems do not have
spaces in the channel names like the original Vectorview systems
did.
-.. note:: The mne_make_eeg_layout utility can be employed to create a layout file matching the positioning of EEG electrodes, see Section 11.6.
+.. note:: The mne_make_eeg_layout utility can be employed to create a layout file matching the positioning of EEG electrodes, see :ref:`CHDDGDJA`.
.. _CACDDIDH:
@@ -1778,7 +1778,7 @@ layouts reside in ``$MNE_ROOT/share/mne/mne_analyze/lout`` .
In addition any layout files residing in ``$HOME/.mne/lout`` are listed.
The format of the layout files is the same as for the Neuromag programs xplotter and xfit .
A custom EEG layout can be easily created with the mne_make_eeg_layout utility,
-see Section 11.6.
+see :ref:`CHDDGDJA`.
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 72d6b48..b946733 100644
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -467,7 +467,7 @@ but can be added, together with other channels, with the ``--type`` .
The channels from 160 onwards are designated as miscellaneous input
channels (MISC 001, MISC 002, etc.). The channel names and types
of these channels can be afterwards changed with the mne_rename_channels utility,
-see Section 11.4.5. In addition, it is possible to synthesize
+see :ref:`CHDCFEAJ`. In addition, it is possible to synthesize
the digital trigger channel (STI 014) from available analog
trigger channel data, see the ``--stim`` option, below.
The synthesized trigger channel data value at sample INLINE_EQUATION will
@@ -702,13 +702,13 @@ the EDF/EDF+/BDF file is converted to the fif format in MNE:
digitized electrode location associated with them. If these channels
are used for EOG or EMG measurements, their channel types should
be changed to the correct ones using the mne_rename_channels utility,
- see Section 11.4.5. EEG channels which do not have a location
+ see :ref:`CHDCFEAJ`. EEG channels which do not have a location
associated with them should be assigned to be MISC channels.
- After the channel types are correctly defined, a topographical
layout file can be created for mne_browse_raw and mne_analyze using
the mne_make_eeg_layout utility,
- see Section 11.6.
+ see :ref:`CHDDGDJA`.
- The trigger channel name in BDF files is "Status".
This must be specified with the --digtrig option or with help of
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index 85ab501..2996265 100644
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -36,7 +36,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_compute_mne* | Computes the minimum-norm estimates, |
| | see Section B.3.1. Most of the |
| | functionality of mne_compute_mne is |
- | | included in mne_make_movie . |
+ | | included in mne_make_movie. |
+----------------------------+--------------------------------------------+
| *mne_compute_raw_inverse* | Compute the inverse solution from raw data |
| | see :ref:`CBBCGHAH`. |
@@ -76,7 +76,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+----------------------------+--------------------------------------------+
| mne_redo_file_nocwd | Works like mne_redo_file but does not try |
| | to change in to the working directory |
- | | specified in the 'production environment' |
+ | | specified in the 'production environment'. |
+----------------------------+--------------------------------------------+
| *mne_setup_forward_model* | Set up the BEM-related fif files, |
| | see Section 3.7. |
@@ -101,23 +101,23 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| Name | Purpose |
+=================================+============================================+
| *mne_add_patch_info* | Add neighborhood information to a source |
- | | space file, see Section 11.7. |
+ | | space file, see :ref:`BEHCBCGG`. |
+---------------------------------+--------------------------------------------+
| *mne_add_to_meas_info* | Utility to add new information to the |
| | measurement info block of a fif file. The |
| | source of information is another fif file. |
+---------------------------------+--------------------------------------------+
| *mne_add_triggers* | Modify the trigger channel STI 014 in a raw|
- | | data file, see Section 11.4.6. The same |
+ | | data file, see :ref:`CHDBDDDF`. The same |
| | effect can be reached by using an event |
| | file for averaging in mne_process_raw and |
| | mne_browse_raw. |
+---------------------------------+--------------------------------------------+
| *mne_annot2labels* | Convert parcellation data into label files,|
- | | see Section 11.14. |
+ | | see :ref:`CHDEDHCG`. |
+---------------------------------+--------------------------------------------+
| *mne_anonymize* | Remove subject-specific information from a |
- | | fif data file, see Section 11.4.7. |
+ | | fif data file, see :ref:`CHDIJHIC`. |
+---------------------------------+--------------------------------------------+
| *mne_average_forward_solutions* | Calculate an average of forward solutions, |
| | see Section 5.10. |
@@ -127,7 +127,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+---------------------------------+--------------------------------------------+
| *mne_change_baselines* | Change the dc offsets according to |
| | specifications given in a text file, |
- | | see Section 11.12. |
+ | | see :ref:`CHDDIDCC`. |
+---------------------------------+--------------------------------------------+
| *mne_change_nave* | Change the number of averages in an |
| | evoked-response data file. This is often |
@@ -137,7 +137,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_check_eeg_locations* | Checks that the EEG electrode locations |
| | have been correctly transferred from the |
| | Polhemus data block to the channel |
- | | information tags, see Section 11.4.3. |
+ | | information tags, see :ref:`CHDJGGGC`. |
+---------------------------------+--------------------------------------------+
| *mne_check_surface* | Check the validity of a FreeSurfer surface |
| | file or one of the surfaces within a BEM |
@@ -165,7 +165,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+---------------------------------+--------------------------------------------+
| *mne_cov2proj* | Pick eigenvectors from a covariance matrix |
| | and create a signal-space projection (SSP) |
- | | file out of them, see Section 11.9. |
+ | | file out of them, see :ref:`CHDECHBF`. |
+---------------------------------+--------------------------------------------+
| *mne_create_comp_data* | Create a fif file containing software |
| | gradient compensation information from a |
@@ -197,10 +197,10 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | system to fif format, see Section 9.2.11. |
+---------------------------------+--------------------------------------------+
| *mne_fit_sphere_to_surf* | Fit a sphere to a surface given in either |
- | | fif or FreeSurfer format, see Section 11.9.|
+ | | fif or FreeSurfer format, see :ref:`CHDECHBF`.|
+---------------------------------+--------------------------------------------+
| *mne_fix_mag_coil_types* | Update the coil types for magnetometers |
- | | in a fif file, see :ref:`CHDGAAJC` |
+ | | in a fif file, see :ref:`CHDGAAJC`. |
+---------------------------------+--------------------------------------------+
| *mne_fix_stim14* | Fix coding errors of trigger channel |
| | STI 014, see Section 3.9.1. |
@@ -211,7 +211,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_insert_4D_comp* | Read Magnes compensation channel data from |
| | a text file and merge it with raw data |
| | from other channels in a fif file, see |
- | | Section 9.2.5 |
+ | | Section 9.2.5. |
+---------------------------------+--------------------------------------------+
| *mne_list_bem* | List BEM information in text format, |
| | see Section 9.6. |
@@ -228,7 +228,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | Neuromag MRIlab software, see Section 9.5. |
+---------------------------------+--------------------------------------------+
| *mne_list_versions* | List versions and compilation dates of MNE |
- | | software modules, see Section 11.2. |
+ | | software modules, see :ref:`CHDFIGBG`. |
+---------------------------------+--------------------------------------------+
| *mne_make_cor_set* | Used by mne_setup_mri to create fif format |
| | MRI description files from COR or mgh/mgz |
@@ -237,11 +237,11 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | in :ref:`BABBHHHE`. |
+---------------------------------+--------------------------------------------+
| *mne_make_derivations* | Create a channel derivation data file, see |
- | | Section 11.5. |
+ | | :ref:`CHDHJABJ`. |
+---------------------------------+--------------------------------------------+
| *mne_make_eeg_layout* | Make a topographical trace layout file |
| | using the EEG electrode locations from |
- | | an actual measurement, see Section 11.6. |
+ | | an actual measurement, see :ref:`CHDDGDJA`.|
+---------------------------------+--------------------------------------------+
| *mne_make_morph_maps* | Precompute the mapping data needed for |
| | morphing between subjects, see |
@@ -268,20 +268,20 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | see Section 9.13. |
+---------------------------------+--------------------------------------------+
| *mne_rename_channels* | Change the names and types of channels |
- | | in a fif file, see Section 11.4.5. |
+ | | in a fif file, see :ref:`CHDCFEAJ`. |
+---------------------------------+--------------------------------------------+
| *mne_sensitivity_map* | Compute a sensitivity map and output |
| | the result in a w-file, |
- | | see Section 11.10. |
+ | | see :ref:`CHDDCBGI`. |
+---------------------------------+--------------------------------------------+
| *mne_sensor_locations* | Create a file containing the sensor |
| | locations in text format. |
+---------------------------------+--------------------------------------------+
| *mne_show_fiff* | List contents of a fif file, |
- | | see Section 11.3 |
+ | | see :ref:`CHDHEDEF`. |
+---------------------------------+--------------------------------------------+
| *mne_simu* | Simulate MEG and EEG data, |
- | | see Section 11.13. |
+ | | see :ref:`CHDECAFD`. |
+---------------------------------+--------------------------------------------+
| *mne_smooth* | Smooth a w or stc file. |
+---------------------------------+--------------------------------------------+
@@ -294,7 +294,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | ignored skips or vice versa. |
+---------------------------------+--------------------------------------------+
| *mne_transform_points* | Transform between MRI and MEG head |
- | | coordinate frames, see Section 11.11. |
+ | | coordinate frames, see :ref:`CHDDDJCA`. |
+---------------------------------+--------------------------------------------+
| *mne_tufts2fiff* | Convert EEG data from the Tufts |
| | University format to fif format, |
@@ -417,16 +417,16 @@ listed in :ref:`CIHDGFAA`
+-------------------------+--------------------------------------------+
| Name of the variable | Description |
+=========================+============================================+
- | MNE_ROOT | Location of the MNE software, see above |
+ | MNE_ROOT | Location of the MNE software, see above. |
+-------------------------+--------------------------------------------+
| FREESURFER_HOME | Location of the FreeSurfer software. |
| | Needed during FreeSurfer reconstruction |
| | and if the FreeSurfer MRI viewer is used |
| | with mne_analyze, see :ref:`CACCHCBF`. |
+-------------------------+--------------------------------------------+
- | SUBJECTS_DIR | Location of the MRI data |
+ | SUBJECTS_DIR | Location of the MRI data. |
+-------------------------+--------------------------------------------+
- | SUBJECT | Name of the current subject |
+ | SUBJECT | Name of the current subject. |
+-------------------------+--------------------------------------------+
| MNE_TRIGGER_CH_NAME | Name of the trigger channel in raw data, |
| | see Section 4.2.1. |
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index 954912a..7285c93 100644
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -264,7 +264,7 @@ they are listed in :ref:`BGBEFADJ`.
mne_ex_read_write_raw Example of processing raw data (read and write).
========================= =================================================================================
-.. note:: In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called *processing history* block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appr [...]
+.. note:: In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called *processing history* block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appr [...]
Some data structures
####################
@@ -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 Section 11.7.2. 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 ed3b64d..5404ae9 100644
--- a/doc/source/manual/mne.rst
+++ b/doc/source/manual/mne.rst
@@ -282,7 +282,7 @@ Cortical patch statistics
If the ``--cps`` option was used in source space
creation (see Section 3.5) or if mne_add_patch_info described
-in Section 11.7 was run manually the source space file
+in :ref:`BEHCBCGG` was run manually the source space file
will contain for each vertex of the cortical surface the information
about the source space point closest to it as well as the distance
from the vertex to this source space point. The vertices for which
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index afc1d0f..51e2b64 100644
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -218,7 +218,7 @@ commands:
``mne_make_eeg_layout --fif sample_audvis_raw.fif --lout $HOME/.mne/lout/sample-EEG.lout``
-Please refer to Section 11.6 for more information
+Please refer to :ref:`CHDDGDJA` for more information
on mne_make_eeg_layout .
.. note:: It is usually sufficient to create one EEG layout for each electrode cap you are using in your experiment rather than using a different layout file for each data file generated using the same cap.
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
index 702716d..43b2de5 100644
--- a/doc/source/manual/utilities.rst
+++ b/doc/source/manual/utilities.rst
@@ -610,7 +610,7 @@ The command-line options are:
.. _BEHCBCGG:
-Adding neighborhood information to source spaces
+Adding neighborhood/topology information to source spaces
################################################
Purpose
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