[med-svn] [python-mne] 149/376: 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 961b0875997a7b5c1f5cc663c52b25f0ab4d83ea
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Fri Mar 18 12:05:45 2011 -0400
fixing manual
---
doc/source/manual/analyze.rst | 6 +++---
doc/source/manual/cookbook.rst | 4 ++--
doc/source/manual/forward.rst | 12 ++++++------
doc/source/manual/list.rst | 14 +++++++-------
doc/source/manual/matlab.rst | 2 +-
doc/source/manual/mne.rst | 16 ++++++++--------
doc/source/manual/sampledata.rst | 8 ++++----
7 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index 405dfba..c57d5b9 100644
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -266,7 +266,7 @@ is shown in :ref:`CACFDIJJ`:
**Lights...**
Adjust the lighting of the scenes in the main display and the viewer, see
- Sections :ref:`CACBHDBF` and :ref:`CACEFFJF`.
+ :ref:`CACBHDBF` and :ref:`CACEFFJF`.
**Field mapping...**
@@ -1114,7 +1114,7 @@ from the option menu labelled Output mode :
**Snapshot**
A new image file is produced every time ``s`` is pressed
- in the image window, see Sections :ref:`CACCABEA` and :ref:`CACFDDCB`. The image file name is used as the stem of
+ in the image window, see :ref:`CACCABEA` and :ref:`CACFDDCB`. The image file name is used as the stem of
the output files. For example, if the name is, ``sample.jpg`` ,
the output files will be ``sample_shot_001.jpg`` , ``sample_shot_002.jpg`` , *etc.*
@@ -2343,7 +2343,7 @@ The saving and loading choices are:
Loads the MEG/MRI coordinate transformation from the file specified.
The MEG/MRI coordinate transformation files are employed
-in the forward calculations. The convenience script mne_do_forward solution described in Section 3.11 uses
+in the forward calculations. The convenience script mne_do_forward solution described in :ref:`BABCHEJD` uses
a search sequence which is compatible with the file naming conventions
described above. It is recommended that -trans.fif file
saved with the Save default and Save... options
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
index 2b84d84..b382383 100644
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -532,7 +532,7 @@ fix is included as the first raw data processing step. Note, however,
the mne_browse_raw and mne_process_raw always sets
the calibration factor to one internally.
-.. note:: If your data file was acquired on or after November 10, 2005 on the Martinos center Vectorview system, it is not necessary to use mne_fix_stim14 .
+.. note:: If your data file was acquired on or after November 10, 2005 on the Martinos center Vectorview system, it is not necessary to use mne_fix_stim14 .
.. _BABCDFJH:
@@ -652,7 +652,7 @@ the Neuromag MEG-MRI integration tool. Section 3.3.1 of the MRIlab User's
Guide, Neuromag P/N NM20419A-A contains a detailed description of
this task. Employ the images in the set ``mri/T1-neuromag/sets/COR.fif`` for
the alignment. Check the alignment carefully using the digitization
-data included in the measurement file as described in :ref:`BJEBIBAI`.1
+data included in the measurement file as described in Section 5.3.1
of the above manual. Save the aligned description file in the same
directory as the original description file without the alignment
information but under a different name.
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index c0a3bd9..14b9665 100644
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -201,7 +201,7 @@ Creating a surface-based source space
The fif format source space files containing the dipole locations
and orientations are created with the utility mne_make_source_space .
This utility is usually invoked by the convenience script mne_setup_source_space ,
-see Section 3.5.
+see :ref:`CIHCHDAE`.
The command-line options are:
@@ -387,7 +387,7 @@ conductivity information so that it can be employed in the BEM calculations.
.. note:: The utility mne_tri2fiff previously used for this task has been replaced by mne_surf2bem .
-.. note:: The convenience script mne_setup_forward_model described in Section 3.7 calls mne_surf2bem with the appropriate options.
+.. note:: The convenience script mne_setup_forward_model described in :ref:`CIHDBFEG` calls mne_surf2bem with the appropriate options.
.. note:: The vertices of all surfaces should be given in the MRI coordinate system.
@@ -571,7 +571,7 @@ Computing the BEM geometry data
The utility mne_prepare_bem_model computes
the geometry information for BEM. This utility is usually invoked
by the convenience script mne_setup_forward_model ,
-see Section 3.7. The command-line options are:
+see :ref:`CIHDBFEG`. The command-line options are:
**\---bem <name>**
@@ -579,7 +579,7 @@ see Section 3.7. The command-line options are:
surfaces and the conductivities of the compartments. The standard
ending for this file is ``-bem.fif`` and it is produced
either with the utility mne_surf2bem (:ref:`BEHCACCJ`) or the convenience script mne_setup_forward_model ,
- see Section 3.7.
+ see :ref:`CIHDBFEG`.
**\---sol <name>**
@@ -940,7 +940,7 @@ In this approach, the convenience of the automatic file naming conventions
present in mne_do_forward_solution are
lost. However, there are some special-purpose options available
in mne_forward_solution only.
-Please refer to Section 3.11 for information on mne_do_forward_solution .
+Please refer to :ref:`BABCHEJD` for information on mne_do_forward_solution.
.. _BJEIGFAE:
@@ -1039,7 +1039,7 @@ the following command-line options:
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 Section 3.10. These files typically reside in ``$SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets`` .
+ outlined in :ref:`CHDBEHDC`. These files typically reside in ``$SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets`` .
**\---trans <name>**
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index a5e297e..c14db82 100644
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -44,11 +44,11 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_convert_mne_data* | Convert MNE data files to other file |
| | formats, see Section 9.12. |
+----------------------------+--------------------------------------------+
- | *mne_do_forward_solution* | Convenience script to calculate the forwar |
- | | solution matrix, see Section 3.11. |
+ | *mne_do_forward_solution* | Convenience script to calculate the forward|
+ | | solution matrix, see :ref:`BABCHEJD`. |
+----------------------------+--------------------------------------------+
| *mne_do_inverse_operator* | Convenience script to compute the inverse |
- | | operator decomposition, see Section 3.13. |
+ | | operator decomposition, see :ref:`CIHCFJEI`.|
+----------------------------+--------------------------------------------+
| *mne_forward_solution* | Calculate the forward solution matrix, see |
| | Section 5.9. |
@@ -79,11 +79,11 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | specified in the 'production environment'. |
+----------------------------+--------------------------------------------+
| *mne_setup_forward_model* | Set up the BEM-related fif files, |
- | | see Section 3.7. |
+ | | see :ref:`CIHDBFEG`. |
+----------------------------+--------------------------------------------+
| *mne_setup_mri* | A convenience script to create the fif |
| | files describing the anatomical MRI data, |
- | | see Section 3.4. |
+ | | see :ref:`BABCCEHF` |
+----------------------------+--------------------------------------------+
| *mne_setup_source_space* | A convenience script to create a source |
| | space description file, see Section 3.5. |
@@ -203,7 +203,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | in a fif file, see :ref:`CHDGAAJC`. |
+---------------------------------+--------------------------------------------+
| *mne_fix_stim14* | Fix coding errors of trigger channel |
- | | STI 014, see Section 3.9.1. |
+ | | STI 014, see :ref:`BABCDBDI`. |
+---------------------------------+--------------------------------------------+
| *mne_flash_bem* | Create BEM tessellation using multi-echo |
| | FLASH MRI data, see Section A.2. |
@@ -232,7 +232,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+---------------------------------+--------------------------------------------+
| *mne_make_cor_set* | Used by mne_setup_mri to create fif format |
| | MRI description files from COR or mgh/mgz |
- | | format MRI data, see Section 3.4. The |
+ | | format MRI data, see :ref:`BABCCEHF`. The |
| | mne_make_cor_set utility is described |
| | in :ref:`BABBHHHE`. |
+---------------------------------+--------------------------------------------+
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index 7285c93..ae4a305 100644
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -14,7 +14,7 @@ facilitate interfacing with binary file formats of the MNE software.
The toolbox is located at ``$MNE_ROOT/share/matlab`` . The
names of the MNE Matlab toolbox functions begin either with mne_ or
with fiff_ . When you source the mne_setup script
-as described in Section 2.4 on of the following actions
+as described in :ref:`CIHCDHGI`, one of the following actions
takes place:
- If you do not have the Matlab startup.m
diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst
index 5404ae9..c3307c7 100644
--- a/doc/source/manual/mne.rst
+++ b/doc/source/manual/mne.rst
@@ -165,7 +165,7 @@ be adjusted with the regularization options ``--magreg`` , ``--gradreg`` ,
and ``--eegreg`` specified at the time of the inverse operator
decomposition, see :ref:`CBBDDBGF`. The convenience script mne_do_inverse_solution has
the ``--magreg`` and ``--gradreg`` combined to
-a sigle option, ``--megreg`` , see Section 3.13.
+a sigle option, ``--megreg`` , see :ref:`CIHCFJEI`.
Suggested range of values for INLINE_EQUATION is INLINE_EQUATION.
.. _CHDBEHBC:
@@ -281,7 +281,7 @@ Cortical patch statistics
=========================
If the ``--cps`` option was used in source space
-creation (see Section 3.5) or if mne_add_patch_info described
+creation (see :ref:`CIHCHDAE`) or if mne_add_patch_info described
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
@@ -476,8 +476,8 @@ 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 Section 3.5. Blaa
- blaa...
+ have the patch information computed, see :ref:`CIHCHDAE`. Blaa
+ blaa...**what???**
**\---fwd <name>**
@@ -530,17 +530,17 @@ The command-line options of ``mne_inverse_operator`` are:
**\---depth**
- Employ depth weighting. For details, see Section :ref:`CBBDFJIE`.
+ Employ depth weighting. For details, see :ref:`CBBDFJIE`.
**\---weightexp <value>**
This parameter determines the steepness of the depth weighting function
- (default = 0.8). For details, see Section :ref:`CBBDFJIE`.
+ (default = 0.8). For details, see :ref:`CBBDFJIE`.
**\---weightlimit <value>**
Maximum relative strength of the depth weighting (default = 10). For
- details, see Section :ref:`CBBDFJIE`.
+ details, see :ref:`CBBDFJIE`.
**\---fmri <name>**
@@ -621,7 +621,7 @@ The command-line options of ``mne_inverse_operator`` are:
statistics for the source space. Since this computation is time consuming,
it is recommended that the patch statistics are precomputed and
the source space file containing the patch information is employed
- already when the forward solution is computed, see Sections 3.5 and 3.11.
+ already when the forward solution is computed, see :ref:`CIHCHDAE` and Section 3.11.
For technical details of the patch information, please consult :ref:`CBBDBHDI`. This option is considered experimental at
the moment.
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index 51e2b64..3be8145 100644
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -166,7 +166,7 @@ MRI viewer, MRIlab, say
``mne_setup_mri``
This command sets up the directories ``subjects/sample/mri/T1-neuromag`` and ``subjects/sample/mri/brain-neuromag`` .
-For more information, see Section 3.4.
+For more information, see :ref:`BABCCEHF`.
.. _CHDIGEJG:
@@ -178,7 +178,7 @@ The source space with a 5-mm grid spacing is set up by saying:
``mne_setup_source_space --ico -6``
This command sets up the source-space related files in directory ``subjects/sample/bem`` as
-described in Section 3.5.
+described in :ref:`CIHCHDAE`.
.. _CHDJDGBD:
@@ -191,7 +191,7 @@ model are accomplished with the command:
``mne_setup_forward_model --homog --surf --ico 4``
This command sets up the homogeneous BEM-model related files
-in directory ``subjects/sample/bem`` as described in section Section 3.7. In
+in directory ``subjects/sample/bem`` as described in :ref:`CIHDBFEG`. In
addition to the homogeneous BEM, you also need the three-layer BEM model,
which can be used for both EEG and MEG:
@@ -665,7 +665,7 @@ of the MNEs and dSPMs is accomplished by the command:
This produces a depth-weighted inverse operator decomposition
with 'loose' orientation constraint applied. More
details on the convenience script mne_do_inverse_operator are
-provided in Section 3.13.
+provided in :ref:`CIHCFJEI`.
The above command employs both EEG and MEG data. To create
separate solution for EEG and MEG, run the commands:
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