[med-svn] [python-mne] 151/376: 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 3e4d074c1805eca35085185449f22d89770eb9d0
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Mon Mar 21 11:57:11 2011 -0400
fixing manual
---
doc/source/manual/analyze.rst | 12 ++++++------
doc/source/manual/convert.rst | 8 ++++----
doc/source/manual/list.rst | 24 ++++++++++++------------
doc/source/manual/matlab.rst | 6 +++---
4 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index fcd1148..b9ab3a2 100644
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -936,7 +936,7 @@ includes the following lines:
Shows the location in the *FreeSurfer* Talairach
coordinates which give a better match to the Talairach atlas.
-The above coordinate systems are discussed in detail in Section 5.2.
+The above coordinate systems are discussed in detail in :ref:`CHDEDFIB`.
.. note:: By default, the tksurfer program, part of the FreeSurfer package, shows the vertex locations on the *orig* rather than *white* surfaces. Therefore, the coordinates shown in mne_analyze and tksurfer are by default slightly different (usually by < 1 mm). To make the two programs consistent, you can start tksurfer with the ``-orig white`` option.
@@ -1176,13 +1176,13 @@ the subject's FreeSurfer directory. This surface is automatically
prepared if you use the watershed algorithm as described in Section A.1.
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 Section 5.6.
+the fif format scalp surface file, see :ref:`BEHCACCJ`.
If a file called ``bem/`` <subject>``-bem.fif`` under
the subject's FreeSurfer directory is present, mne_analyze tries
to load the BEM surface triangulations from there. This file can
be a symbolic link to one of the ``-bem.files`` created
-by mne_prepare_bem_model , see Section 5.7.
+by mne_prepare_bem_model , see :ref:`CHDJFHEB`.
If the BEM file contains a head surface triangulation, it will be
used instead of the one present in the ``bem/`` <subject>``-head.fif`` file.
@@ -1984,12 +1984,12 @@ specifies the forward model to be used:
**EEG scalp radius [mm]**
Specifies the radius of the outermost shell in the EEG sphere model. For
- details, see Section 5.9.4.
+ details, see :ref:`CHDIAFIG`.
**EEG sphere model name**
Specifies the name of the EEG sphere model to use. For details,
- see Section 5.9.4.
+ see :ref:`CHDIAFIG`.
**BEM model**
@@ -2002,7 +2002,7 @@ specifies the forward model to be used:
**Accurate field calculation**
- Switches on the more accurate geometry definition of MEG coils, see Section 5.8.
+ Switches on the more accurate geometry definition of MEG coils, see :ref:`BJEIAEIE`.
In dipole fitting, there is very little difference between the *accurate* and *normal* coil
geometry definitions.
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
index 47bd8f9..0557940 100644
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -991,7 +991,7 @@ Converting volumetric data into an MRI overlay
##############################################
With help of the mne_volume_source_space utility
-(Section 5.5) it is possible to create a source space which
+(:ref:`BJEFEHJI`) it is possible to create a source space which
is defined within a volume rather than a surface. If the ``--mri`` option
was used in mne_volume_source_space , the
source space file contains an interpolator matrix which performs
@@ -1207,7 +1207,7 @@ the following command-line options:
**\---tri <name>**
- Specifies a text format input file. The format of this file is described in Section 5.6.3.
+ Specifies a text format input file. The format of this file is described in :ref:`BEHDEFCD`.
**\---meters**
@@ -1295,7 +1295,7 @@ the following command-line options:
**\---triout <name>**
Specifies an ASCII output file that will contain the surface data
- in the triangle file format desribed in Section 5.6.3.
+ in the triangle file format desribed in :ref:`BEHDEFCD`.
**\---pntout <name>**
@@ -1367,7 +1367,7 @@ data as input. The command-line options are:
the talairach.xfm file referred to in the MRI volume, and the the
fixed transforms INLINE_EQUATION and INLINE_EQUATION will
added to the output file. For definition of the coordinate transformations,
- see Section 5.2.
+ see :ref:`CHDEDFIB`.
**\---talairach <name>**
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index ed55bef..1be7747 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`. |
@@ -47,11 +47,11 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *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 :ref:`CIHCFJEI`.|
+ | *mne_do_inverse_operator* | Convenience script for inverse operator |
+ | | decomposition, see :ref:`CIHCFJEI`. |
+----------------------------+--------------------------------------------+
| *mne_forward_solution* | Calculate the forward solution matrix, see |
- | | Section 5.9. |
+ | | :ref:`CHDDIBAH`. |
+----------------------------+--------------------------------------------+
| mne_inverse_operator | Compute the inverse operator decomposition |
| | see Section 6.4. |
@@ -60,7 +60,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | :ref:`CBBECEDE`. |
+----------------------------+--------------------------------------------+
| *mne_make_source_space* | Create a *fif* source space description |
- | | file, see Section 5.4. |
+ | | file, see :ref:`BEHCGJDD`. |
+----------------------------+--------------------------------------------+
| *mne_process_raw* | A batch-mode version of mne_browse_raw, |
| | see :ref:`ch_browse`. |
@@ -120,7 +120,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | fif data file, see :ref:`CHDIJHIC`. |
+---------------------------------+--------------------------------------------+
| *mne_average_forward_solutions* | Calculate an average of forward solutions, |
- | | see Section 5.10. |
+ | | see :ref:`CHDBBFCA`. |
+---------------------------------+--------------------------------------------+
| *mne_brain_vision2fiff* | Convert EEG data from BrainVision format |
| | to fif format, see Section 9.2.10. |
@@ -196,8 +196,8 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_eximia2fiff* | Convert EEG data from the Nexstim eXimia |
| | 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 :ref:`CHDECHBF`.|
+ | *mne_fit_sphere_to_surf* | Fit a sphere to a surface given in 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`. |
@@ -218,7 +218,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+---------------------------------+--------------------------------------------+
| *mne_list_coil_def* | Create the coil description file. This |
| | is run automatically at when the software |
- | | is set up, see Section 5.8.5. |
+ | | is set up, see :ref:`BJEHHJIJ`. |
+---------------------------------+--------------------------------------------+
| *mne_list_proj* | List signal-space projection data from a |
| | fif file. |
@@ -260,7 +260,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | directories, see Section A.2.1. |
+---------------------------------+--------------------------------------------+
| *mne_prepare_bem_model* | Perform the geometry calculations for |
- | | BEM forward solutions, see Section 5.7. |
+ | | BEM forward solutions, see :ref:`CHDJFHEB`.|
+---------------------------------+--------------------------------------------+
| mne_process_stc | Manipulate stc files. |
+---------------------------------+--------------------------------------------+
@@ -288,7 +288,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_surf2bem* | Create a *fif* file describing the |
| | triangulated compartment boundaries for |
| | the boundary-element model (BEM), |
- | | see Section 5.6. |
+ | | see :ref:`BEHCACCJ`. |
+---------------------------------+--------------------------------------------+
| *mne_toggle_skips* | Change data skip tags in a raw file into |
| | ignored skips or vice versa. |
@@ -309,7 +309,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | overlay, see Section 9.4. |
+---------------------------------+--------------------------------------------+
| *mne_volume_source_space* | Make a volumetric source space, |
- | | see Section 5.5. |
+ | | see :ref:`BJEFEHJI`. |
+---------------------------------+--------------------------------------------+
| *mne_watershed_bem* | Do the segmentation for BEM using the |
| | watershed algorithm, see Section A.1. |
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index ae4a305..4c71906 100644
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -312,7 +312,7 @@ The documented structures are:
The coil definition structure useful for forward calculations and array
visualization, see :ref:`BGBGBEBH`. For more detailed information on
- coil definitions, see Section 5.8.
+ coil definitions, see :ref:`BJEIAEIE`.
**ch**
@@ -523,7 +523,7 @@ The documented structures are:
.. _BGBGBEBH:
-.. table:: The coildef structure. For more detailed information, see Section 5.8.
+.. table:: The coildef structure. For more detailed information, see :ref:`BJEIAEIE`.
============== ======================= ========================================================================================
Field Data type Description
@@ -677,7 +677,7 @@ The documented structures are:
nsource int32 Total number of source space points.
nchan int32 Number of channels.
sol named matrix The forward solution matrix.
- sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see Section 5.9.6. This field is present only if the forward solution was computed with the ``--grad`` option, see Section 5.9.2.
+ sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see :ref:`BJEFEJJG`. This field is present only if the forward solution was computed with the ``--grad`` option, see :ref:`BJEIGFAE`.
mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
src surf(*) The description of the source spaces
source_rr double(nsource,3) The source locations.
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