[med-svn] [python-mne] 180/376: fixing manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:32 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 243a14410ec561b93544ac46be3524b1e3427317
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Thu Mar 31 16:32:42 2011 -0400
fixing manual
---
doc/source/manual/AppA.rst | 4 +-
doc/source/manual/AppEULA.rst | 4 +-
doc/source/manual/AppInstall.rst | 8 ++--
doc/source/manual/AppReleaseNotes.rst | 86 +++++++++++++++++------------------
doc/source/manual/analyze.rst | 2 +-
doc/source/manual/cookbook.rst | 6 +--
doc/source/manual/intro.rst | 14 +++---
doc/source/manual/list.rst | 14 +++---
doc/source/manual/sampledata.rst | 4 +-
9 files changed, 71 insertions(+), 71 deletions(-)
diff --git a/doc/source/manual/AppA.rst b/doc/source/manual/AppA.rst
index 2b14ea8..ac4f09b 100755
--- a/doc/source/manual/AppA.rst
+++ b/doc/source/manual/AppA.rst
@@ -54,7 +54,7 @@ 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
-described Chapter 7 looks for this file the visualizations
+described :ref:`ch_interactive_analysis` looks for this file the visualizations
involving the scalp surface.
.. _BABFCDJH:
@@ -319,7 +319,7 @@ For further information, see http://brainsuite.usc.edu/.
The conversion of BrainSuite tessellation
files to MNE software compatible formats is accomplished with the mne_convert_surface utility,
-covered in Section 9.7.
+covered in :ref:`BEHDIAJG`.
The workflow needed to employ the BrainSuite tessellations
is:
diff --git a/doc/source/manual/AppEULA.rst b/doc/source/manual/AppEULA.rst
index 69eea49..ebf17b3 100755
--- a/doc/source/manual/AppEULA.rst
+++ b/doc/source/manual/AppEULA.rst
@@ -124,8 +124,8 @@ affiliated with such individual at the time of such download (the "Institution")
- *General.* This Agreement constitutes
the entire understanding between you and Licensor with respect to
the subject matter hereof, and supercedes any prior or contemporaneous
- oral or written agreements with respect thereto. Sections 2, 4,
- 6, 8, 9, 11 shall survive any termination of this Agreement. This
+ oral or written agreements with respect thereto. :ref:`CHDBAFGJ`,:ref:`ch_browse`,
+ :ref:`ch_mne`, :ref:`ch_morph`, :ref:`ch_convert`, and :ref:`ch_misc` shall survive any termination of this Agreement. This
Agreement may be modified or amended only in a writing signed by
duly authorized representatives of both Parties hereto. The invalidity
or unenforceability of any provision of this Agreement shall not
diff --git a/doc/source/manual/AppInstall.rst b/doc/source/manual/AppInstall.rst
index bf467f0..be4759f 100755
--- a/doc/source/manual/AppInstall.rst
+++ b/doc/source/manual/AppInstall.rst
@@ -161,14 +161,14 @@ is to look at the manual:
Chapters of interest for a novice user include:
-- Chapters 1 and 2 contain introduction
+- :ref:`CHDDEFAB` and :ref:`CHDBAFGJ` contain introduction
to the software and setup instructions.
-- Chapter 3 is an overview of the necessary steps to
+- :ref:`ch_cookbook` is an overview of the necessary steps to
compute the cortically constrained minimum-norm solutions.
-- Chapter 12 is a hands-on exercise demonstrating analysis
+- :ref:`ch_sample_data` is a hands-on exercise demonstrating analysis
of the sample data set.
-- Chapter 13 contains a list of useful references for
+- :ref:`ch_reading` contains a list of useful references for
understanding the methods implemented in the MNE software.
diff --git a/doc/source/manual/AppReleaseNotes.rst b/doc/source/manual/AppReleaseNotes.rst
index 49fc87a..f20249f 100755
--- a/doc/source/manual/AppReleaseNotes.rst
+++ b/doc/source/manual/AppReleaseNotes.rst
@@ -15,11 +15,11 @@ Release notes for MNE software 2.4
Manual
======
-The manual has been significantly expanded and reorganized. Chapter 7 describing mne_analyze has
-been added. Chapter 12 contains instructions for analyzing
+The manual has been significantly expanded and reorganized. :ref:`ch_interactive_analysis`describing mne_analyze has
+been added. :ref:`ch_sample_data` contains instructions for analyzing
the sample data set provided with the software. Useful background
-material is listed in Chapter 13. Almost all utility programs
-are now covered in the manual.***do we need to remove all "chapter" references?***
+material is listed in :ref:`ch_reading`. Almost all utility programs
+are now covered in the manual.
General software changes
========================
@@ -51,13 +51,13 @@ File conversion utilities
The following import utilities were added:
- mne_ctf2fiff to
- convert CTF data to the fif format, see Section 9.2.2.
+ convert CTF data to the fif format, see :ref:`BEHDEBCH`.
- mne_tufts2fiff to convert
- EEG data from Tufts university to fif format, see Section 9.2.9.
+ EEG data from Tufts university to fif format, see :ref:`BEHDGAIJ`.
The output of the Matlab conversion utilities was changed
-to use structures. For details, see Sections 9.12, 9.7, and 9.13.
+to use structures. For details, see :ref:`BEHCCEBJ`, :ref:`BEHDIAJG`, and :ref:`BEHCBCGG`.
Matlab tools to import and export w and stc files were added.
@@ -95,7 +95,7 @@ Averaging
The highly inefficient program mne_grand_average has
been removed from the distribution and replaced with the combined
use of mne_make_movie and a new
-averaging program mne_average_estimates , see Section 8.6.
+averaging program mne_average_estimates , see :ref:`CHDFDIFE`.
Release notes for MNE software 2.5
##################################
@@ -105,9 +105,9 @@ Manual
The MNE Matlab toolbox is now covered in a separate chapter.
Change bars are employed to indicate changes in the chapters that
-existed in the previous version of the manual. Note that Chapter 10 describing
+existed in the previous version of the manual. Note that :ref:`ch_matlab` describing
the Matlab toolbox is totally new and change bars have not been
-used there. Furthermore, Appendix B now contains all the
+used there. Furthermore, :ref:`BGBDEIGC` now contains all the
information specific to the Martinos Center.
mne_browse_raw
@@ -140,7 +140,7 @@ There are several improvements in the raw data processor mne_browse_raw/mne_proc
- Text format event files can now be loaded for easy inspection
of rejected epochs, for example.
-- Handling of derived channels has been added, see Sections 4.4.12 and :ref:`CHDHJABJ`.
+- Handling of derived channels has been added, see :ref:`CACFHAFH` and :ref:`CHDHJABJ`.
- SSS information is now transferred to the covariance matrix
output files.
@@ -152,7 +152,7 @@ mne_epochs2mat
This new utility extracts epochs from a raw data file, applies
a bandpass filter to them and outputs them in a format convenient
-for processing in Matlab, see Section 9.14.
+for processing in Matlab, see :ref:`BEHFIDCB`.
mne_analyze
===========
@@ -275,14 +275,14 @@ mne_compensate_data
-------------------
This utility applies or removes CTF software gradient compensation
-from evoked-response data, see Section 9.2.4.
+from evoked-response data, see :ref:`BEHDDFBI`.
mne_insert_4D_comp
------------------
This utility merges 4D Magnes compensation data from a text
file and the main helmet sensor data from a fif file and creates
-a new fif file Section 9.2.5.
+a new fif file :ref:`BEHGDDBH`.
mne_ctf_dig2fiff
----------------
@@ -295,7 +295,7 @@ mne_kit2fiff
------------
The purpose of this new utility is to import data from the
-KIT MEG system, see Section 9.2.7.
+KIT MEG system, see :ref:`BEHBJGGF`.
mne_make_derivations
--------------------
@@ -308,8 +308,8 @@ BEM mesh generation
===================
All information concerning BEM mesh generation has been moved
-to Appendix A. Utilities for BEM mesh generation using
-FLASH images have been added, see Section A.2.
+to :ref:`BGBDEIGC`. Utilities for BEM mesh generation using
+FLASH images have been added, see :ref:`BABFCDJH`.
Matlab toolbox
==============
@@ -329,7 +329,7 @@ features include:
matrices, forward solutions, and inverse operator decompositions
directly from fif files.
-The Matlab toolbox is documented in Chapter 10.
+The Matlab toolbox is documented in :ref:`ch_matlab`.
The mne_div_w utility
has been removed because it is now easy to perform its function
@@ -343,7 +343,7 @@ Manual
The changes described below briefly are documented in the
relevant sections of the manual. Change bars are employed to indicate
-changes with respect to manual version 2.5. Chapter 5 now
+changes with respect to manual version 2.5. :ref:`ch_forward` now
contains a comprehensive discussion of the various coordinate systems
used in MEG/EEG data.
@@ -510,7 +510,7 @@ Improvements in the raw data processor mne_browse_raw /mne_process_raw include:
to the averaging and covariance matrix estimation description files,
see :ref:`CACHACHH` and :ref:`BABECIAH`.
-Detailed information on these changes can be found in Chapter 4.
+Detailed information on these changes can be found in :ref:`ch_browse`.
mne_compute_raw_inverse
-----------------------
@@ -538,7 +538,7 @@ mne_epochs2mat
--------------
The name of the digital trigger channel can be specified
-with the MNE_TRIGGER_CH_NAME environment variable, see Section 9.14. Added
+with the MNE_TRIGGER_CH_NAME environment variable, see :ref:`BEHFIDCB`. Added
the ``--digtrigmask`` option.
mne_forward_solution
@@ -550,14 +550,14 @@ the dipole position coordinates, see :ref:`CHDDIBAH`.
mne_list_bem
------------
-The --surfno option is replaced with the --id option, see Section 9.6.
+The --surfno option is replaced with the --id option, see :ref:`BEHBBEHJ`.
mne_make_cor_set
----------------
Include data from mgh/mgz files to the output automatically.
Include the Talairach transformations from the FreeSurfer data to
-the output file if possible. For details, see Section 9.8.
+the output file if possible. For details, see :ref:`BABBHHHE`.
mne_make_movie
--------------
@@ -610,7 +610,7 @@ Removed the ``--tomrivol`` option.
Matlab toolbox
--------------
-Several new functions were added, see Chapter 10.
+Several new functions were added, see :ref:`ch_matlab`.
.. note:: The matlab function fiff_setup_read_raw has a significant change. The sample numbers now take into account possible intial skip in the file, *i.e.*, the time between the start of the data acquisition and the start of saving the data to disk. The first_samp member of the returned structure indicates the initial skip in samples. If you want your own routines, which assume that initial skip has been removed, perform indentically with the previous version, subt [...]
@@ -621,28 +621,28 @@ mne_collect_transforms
----------------------
This utility collects coordinate transformation information
-from several sources into a single file, see Section 9.9.
+from several sources into a single file, see :ref:`BABBIFIJ`.
mne_convert_dig_data
--------------------
This new utility convertes digitization (Polhemus) data between
-different file formats, see Section 9.3.
+different file formats, see :ref:`BABCJEAD`.
mne_edf2fiff
------------
This is a new utility to convert EEG data from EDF, EDF+,
-and BDF formats to the fif format, see Section 9.2.8.
+and BDF formats to the fif format, see :ref:`BABHDBBD`.
mne_brain_vision2fiff
---------------------
This is a new utility to convert BrainVision EEG data to
-the fif format, see Section 9.2.10. This utility is also
+the fif format, see :ref:`BEHCCCDC`. This utility is also
used by the mne_eximia_2fiff script
to convert EEG data from the Nexstim eXimia EEG system to the fif
-format, see Section 9.2.11.
+format, see :ref:`BEHGCEHH`.
mne_anonymize
-------------
@@ -660,7 +660,7 @@ mne_volume_data2mri
-------------------
Convert data defined in a volume created with mne_volume_source_space to
-an MRI overlay, see Section 9.4.
+an MRI overlay, see :ref:`BEHDEJEC`.
mne_volume_source_space
-----------------------
@@ -669,7 +669,7 @@ Create a a grid of source points within a volume, see :ref:`BJEFEHJI`. mne_volum
optionally creates a trilinear interpolator matrix to facilitate
converting values a distribution in the volume grid into an MRI
overlay using mne_volume_data2mri ,
-see Section 9.4.
+see :ref:`BEHDEJEC`.
mne_copy_processing_history
---------------------------
@@ -709,7 +709,7 @@ MNE software and setup for individual users:
- The setup scripts have changed.
The installation and user-level effects of the new software
-organization are discussed in Chapter 2 and Appendix C.
+organization are discussed in :ref:`CHDBAFGJ` and :ref:`BGBDEIGC`.
In addition, several minor bugs have been fixed in the source
code. Most relevant changes visible to the user are listed below.
@@ -732,10 +732,10 @@ mne_browse_raw
==============
- Rejection criteria to detect flat channels
- have been added, see Sections 4.13.2 and 4.14.2.
+ have been added, see :ref:`BABIHFBI` and :ref:`BABCGEJE`.
- Possibility to detect temporal skew between trigger input
- lines has been added, see Sections 4.13.2 and 4.14.2.
+ lines has been added, see :ref:`BABIHFBI` and :ref:`BABCGEJE`.
- --allowmaxshield option now works in the batch mode as well.
@@ -775,16 +775,16 @@ Miscellaneous
has the --orignames option, see :ref:`CHDEIHFA`.
- Added --headcoord option to mne_convert_dig_data ,
- see Section 9.3.
+ see :ref:BABCJEAD`.
- Added --talairach option to mne_make_cor_set ,
- see Section 9.8.
+ see :ref:`BABBHHHE`.
- 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 ,
- see Section 8.5.
+ see :ref:`CHDCEAFC`.
- Added the --blocks and --indent options to mne_show_fiff ,
see :ref:`CHDHEDEF`.
@@ -840,7 +840,7 @@ Miscellaneous
=============
- Added --shift option to mne_convert_surface ,
- see Section 9.7.1.
+ see :ref:`BABEABAA`.
- Added --alpha option to mne_make_movie ,
see :ref:`CBBBBHIF`.
@@ -850,11 +850,11 @@ Miscellaneous
- The fif output from mne_convert_dig_data now
includes the transformation between the digitizer and MNE head coordinate
- systems if such a transformation has been requested, see Section 9.3.
- This also affects the output from mne_eximia2fiff, see Section 9.2.11.
+ 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 ,
- see Section A.2.
+ see :ref:`BABFCDJH`.
Release notes for MNE software 2.7.3
####################################
@@ -867,10 +867,10 @@ Miscellaneous
- The --mghmri option in combination with --surfout inserts
the volume geometry information to the output of mne_convert_surface ,
- see Section 9.7.
+ see :ref:`BEHDIAJG`.
- Added --replacegeom option to mne_convert_surface ,
- see Section 9.7.
+ see :ref:`BEHDIAJG`.
- Modified mne_watershed_bem and mne_flash_bem to
include the volume geometry information to the output. This allows
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index b9ab3a2..82e14d5 100755
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -1173,7 +1173,7 @@ selected, the following additional surfaces will be loaded:
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 Section A.1.
+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`.
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
index 8b7d598..5c44d1a 100755
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -250,14 +250,14 @@ of the intracranial volume. For EEG, the standard model contains
the intracranial space, the skull, and the scalp.
At present, no bulletproof method exists for creating the
-triangulations. Feasible approaches are described in Appendix A.
+triangulations. Feasible approaches are described in :ref:`BGBDEIGC`.
.. _BABDBBFC:
Setting up the triangulation files
==================================
-The segmentation algorithms described in Appendix A produce
+The segmentation algorithms described in :ref:`BGBDEIGC` produce
either FreeSurfer surfaces or triangulation
data in text. Before proceeding to the creation of the boundary
element model, standard files (or symbolic links created with the ``ln -s`` command) have to be present in the subject's ``bem`` directory.
@@ -374,7 +374,7 @@ the following options:
the process is aborted if it is incorrect after taking into account
the state of the swapping. Should this happen, try to run mne_setup_forward_model again including
the ``--noswap`` flag. In particular, if you employ the seglab software
- to create the triangulations (see Appendix A), the ``--noswap`` flag
+ to create the triangulations (see :ref:`BGBDEIGC`), the ``--noswap`` flag
is required. This option is ignored if ``--surf`` is specified
**\---ico <number>**
diff --git a/doc/source/manual/intro.rst b/doc/source/manual/intro.rst
index c449e5e..b5e5cc7 100755
--- a/doc/source/manual/intro.rst
+++ b/doc/source/manual/intro.rst
@@ -15,20 +15,20 @@ Dale, Fischl, Hämäläinen, and others.
The software depends on anatomical MRI processing tools provided
by the FreeSurfer software.
-Chapter 2 of this manual gives an overview of the software
+:ref:`CHDBAFGJ` gives an overview of the software
modules included with MNE software. :ref:`ch_cookbook` is a concise cookbook
describing a typical workflow for a novice user employing the convenience
-scripts as far as possible. Chapters :ref:`ch_browse` to :ref:`ch_misc` give more detailed
+scripts as far as possible. :ref:`ch_browse` to :ref:`ch_misc` give more detailed
information about the software modules. :ref:`ch_sample_data` discusses
processing of the sample data set included with the MNE software. :ref:`ch_reading` lists
some useful background material for the methods employed in the
MNE software.
-Appendix A is an overview of the BEM model mesh
-generation methods, Appendix B contains information specific
-to the setup at Martinos Center of Biomedical Imaging, Appendix C is
-a software installation and configuration guide, Appendix D summarizes
-the software history, and Appendix E contains the End-User
+:ref:`BGBDEIGC` is an overview of the BEM model mesh
+generation methods, :ref:`BGBDEIGC` contains information specific
+to the setup at Martinos Center of Biomedical Imaging, :ref:`BGBDEIGC` is
+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`.
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index 9af0f22..45d04c5 100755
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -34,7 +34,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | see :ref:`ch_browse`. |
+----------------------------+--------------------------------------------+
| *mne_compute_mne* | Computes the minimum-norm estimates, |
- | | see Section B.3.1. Most of the |
+ | | see :ref:`BABDABHI`. Most of the |
| | functionality of mne_compute_mne is |
| | included in mne_make_movie. |
+----------------------------+--------------------------------------------+
@@ -180,7 +180,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_dicom_essentials* | List essential information from a |
| | DICOM file. |
| | This utility is used by the script |
- | | mne_organize_dicom, see Section A.2.1. |
+ | | mne_organize_dicom, see :ref:`BABEBJHI`. |
+---------------------------------+--------------------------------------------+
| *mne_edf2fiff* | Convert EEG data from the EDF/EDF+/BDF |
| | formats to the fif format, |
@@ -206,7 +206,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | STI 014, see :ref:`BABCDBDI`. |
+---------------------------------+--------------------------------------------+
| *mne_flash_bem* | Create BEM tessellation using multi-echo |
- | | FLASH MRI data, see Section A.2. |
+ | | FLASH MRI data, see :ref:`BABFCDJH`. |
+---------------------------------+--------------------------------------------+
| *mne_insert_4D_comp* | Read Magnes compensation channel data from |
| | a text file and merge it with raw data |
@@ -257,7 +257,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | subjects, see :ref:`CHDCEAFC`. |
+---------------------------------+--------------------------------------------+
| *mne_organize_dicom* | Organized DICOM MRI image files into |
- | | directories, see Section A.2.1. |
+ | | directories, see :ref:`BABEBJHI`. |
+---------------------------------+--------------------------------------------+
| *mne_prepare_bem_model* | Perform the geometry calculations for |
| | BEM forward solutions, see :ref:`CHDJFHEB`.|
@@ -312,7 +312,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | see :ref:`BJEFEHJI`. |
+---------------------------------+--------------------------------------------+
| *mne_watershed_bem* | Do the segmentation for BEM using the |
- | | watershed algorithm, see Section A.1. |
+ | | watershed algorithm, see :ref:`BABBDHAG`. |
+---------------------------------+--------------------------------------------+
@@ -398,7 +398,7 @@ For csh/tcsh the corresponding commands are:
``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 Appendix A) and
+on the basis of multi-echo FLASH MRI data (see :ref:`BGBDEIGC`) and
for accessing the tkmedit program
from mne_analyze, see :ref:`CACCHCBF`,
the MNE software needs access to a FreeSurfer license
@@ -435,4 +435,4 @@ listed in :ref:`CIHDGFAA`.
| | values, see :ref:`BABBGJEA`. |
+-------------------------+--------------------------------------------+
-.. note:: Appendix B contains information specific to the setup at the Martinos Center including instructions to access the Neuromag software.
+.. note:: :ref:`BGBDEIGC` contains information specific to the setup at the Martinos Center including instructions to access the Neuromag software.
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index 2a7baa6..1114152 100755
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -144,7 +144,7 @@ in the sample data set:
been computed using the FreeSurfer software.
- The BEM surfaces have been created with the watershed algorithm,
- see Section A.1.
+ see :ref:`BABBDHAG`.
- The MEG/EEG raw data file has been checked with the utilities described
in :ref:`BABCDBDI` and :ref:`BABCDFJH`.
@@ -462,7 +462,7 @@ Observe the following:
- There is a later response in the right parietal area, almost
identical to both visual stimuli.
-.. note:: If you have the Neuromag software available, the averaged data can be also viewed in the Neuromag data plotter (xplotter ). See Section B.2 for instructions on how to use the Neuromag software at the MGH Martinos Center.
+.. note:: If you have the Neuromag software available, the averaged data can be also viewed in the Neuromag data plotter (xplotter ). See :ref:`BABGFDJG` for instructions on how to use the Neuromag software at the MGH Martinos Center.
Computing the noise-covariance matrix
#####################################
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