[med-svn] [python-mne] 230/376: DOC : fix many warnings in doc generation + more conversion
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:52 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 0ef51635d7721a44b7f1ea7a87c4dfa4584c125a
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Tue May 3 12:49:10 2011 -0400
DOC : fix many warnings in doc generation + more conversion
---
doc/Makefile | 1 -
doc/source/getting_started.rst | 2 +-
doc/source/getting_started_at_martinos.rst | 12 +--
doc/source/index.rst | 11 ++-
doc/source/manual.rst | 1 +
doc/source/manual/analyze.rst | 3 +-
doc/source/manual/browse.rst | 57 ++++++------
doc/source/manual/convert.rst | 87 ++++++++++++------
doc/source/manual/cookbook.rst | 6 +-
doc/source/manual/forward.rst | 67 +++++++++-----
doc/source/mne-python.rst | 1 +
doc/source/tutorial.rst | 100 ---------------------
.../plot_cluster_1samp_test_time_frequency.py | 11 +--
.../stats/plot_cluster_stats_time_frequency.py | 13 +--
14 files changed, 169 insertions(+), 203 deletions(-)
diff --git a/doc/Makefile b/doc/Makefile
index 8791073..e1a2a13 100755
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -30,7 +30,6 @@ clean:
-rm -rf build/*
html:
- -rm -rf build/html/_images/*
-rm -rf build/html/_downloads/*1.py
-rm -rf build/html/_downloads/*2.py
-rm -rf build/html/_downloads/*3.py
diff --git a/doc/source/getting_started.rst b/doc/source/getting_started.rst
index b54a0b3..f558020 100755
--- a/doc/source/getting_started.rst
+++ b/doc/source/getting_started.rst
@@ -6,7 +6,7 @@ Getting Started
Inside the Martinos Center
--------------------------
People within the MGH/MIT/HMS Martinos Center should follow
-`internal instructions <getting_started_at_martinos.html>`_.
+:ref:`getting_started_martinos`.
MNE is *already installed* on your system.
diff --git a/doc/source/getting_started_at_martinos.rst b/doc/source/getting_started_at_martinos.rst
index c0ee569..d3b6843 100755
--- a/doc/source/getting_started_at_martinos.rst
+++ b/doc/source/getting_started_at_martinos.rst
@@ -1,19 +1,21 @@
-.. _getting_started:
+.. _getting_started_martinos:
Getting Started at the Martinos Center
======================================
You first need to activate the python scientific environment.
-In a terminal do:
+In a terminal do::
- .. source /usr/pubsw/packages/python/2.6/scientificpython/bin/tcsh_activate
setenv PATH ${PATH}:/usr/pubsw/packages/python/epd/bin
-If you use Bash replace the previous instruction with:
+.. source /usr/pubsw/packages/python/2.6/scientificpython/bin/tcsh_activate
+
+If you use Bash replace the previous instruction with::
- .. source /usr/pubsw/packages/python/2.6/scientificpython/bin/bash_activate
export PATH=${PATH}:/usr/pubsw/packages/python/epd/bin
+.. source /usr/pubsw/packages/python/2.6/scientificpython/bin/bash_activate
+
Then start the python interpreter with:
ipython
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 7e3f16d..4b48bf7 100755
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -7,12 +7,11 @@ MNE is a software package for processing magnetoencephalography data
for reading and writing FIF files produced by Neuromag MEG systems or
converted from other file formats.
-.. * `MNE web site <http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php>`_
-* `Download <http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/MNE_register/index.php>`_ MNE
-* Read the :ref:`manual`.
-* Get started with :ref:`mne_python`
-* :ref:`example_command_line`
-* Join the MNE `mailing list <http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis>`_
+ * `Download <http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/MNE_register/index.php>`_ MNE
+ * Read the :ref:`manual`.
+ * Get started with :ref:`mne_python`
+ * :ref:`example_command_line`
+ * Join the MNE `mailing list <http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis>`_
Manual
======
diff --git a/doc/source/manual.rst b/doc/source/manual.rst
index 2f063e5..9c39ce1 100644
--- a/doc/source/manual.rst
+++ b/doc/source/manual.rst
@@ -24,4 +24,5 @@ Manual
manual/AppInstall
manual/AppReleaseNotes
manual/AppEULA
+ command_line_tutorial
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index f7bccaa..a274485 100755
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -1590,9 +1590,8 @@ controls:
Various options controlling the estimates.
-.. _CACGGICI:
-
.. tabularcolumns:: |p{0.2\linewidth}|p{0.45\linewidth}|
+.. _CACGGICI:
.. table:: The color scale parameters.
+------------+---------------------------------------------------------+
diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst
index 4b4d04f..f93cd6a 100755
--- a/doc/source/manual/browse.rst
+++ b/doc/source/manual/browse.rst
@@ -740,13 +740,13 @@ The items in the dialog have the following functions:
by multiplying the gradiometer scale by this number, yielding units
of fT.
-**EEG (:math:`\mu`V)** EQUATION PROBLEM
+**EEG** (:math:`\mu V`)
- The scale for EEG channels in :math:`\mu`V. EQUATION PROBLEM
+ The scale for EEG channels in :math:`\mu V`.
-**EOG (:math:`\mu`V)** EQUATION PROBLEM
+**EOG** (:math:`\mu V`)
- The scale for EOG channels in :math:`\mu`V. EQUATION PROBLEM
+ The scale for EOG channels in :math:`\mu V`.
**ECG (mV)**
@@ -1038,8 +1038,10 @@ returns to the default layout.
The format of the layout files is:
- <*plot area limits*> <*viewport definition #1*>
-... <*viewport definition #N*>
+ | <*plot area limits*>
+ | <*viewport definition #1*>
+ | ...
+ | <*viewport definition #N*>
The <*plot area limits*> define
the size of the plot area (:math:`x_{min}\ x_{max}\ y_{min}\ y_{max}`) which should accommodate all view ports. When the layout is used, the
@@ -1049,7 +1051,7 @@ a different aspect ratio, there will be empty space on the sides.
The viewports define the locations of the individual channels
in the plot. Each viewport definition consists of
- <*number*> :math:`x_0\ y_0` <*width*> <*height*> <*name*> [: <*name*> ]...
+ <*number*> :math:`x_0\ y_0` <*width*> <*height*> <*name*> [: <*name*> ] ...
where number is a viewport number (not used by the MNE software), :math:`x_0` and :math:`y_0` are
the coordinates of the lower-left corner of the viewport, <*width*> and <*height*> are
@@ -1137,11 +1139,11 @@ The items in the dialog have the following functions:
Rejection criterion for MEG magnetometers and axial gradiometers.
-EEG rejection (:math:`\mu`V) EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
+**EEG rejection** (:math:`\mu V`)
Rejection criterion for EEG channels.
-**EOG rejection (:math:`\mu`V)** EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
+**EOG rejection** (:math:`\mu V`)
Rejection criterion for EOG channels.
@@ -1160,11 +1162,11 @@ EEG rejection (:math:`\mu`V) EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHE
Signal detection criterion for MEG magnetometers and axial gradiometers.
-**EEG no signal (:math:`\mu`V)** EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
+**EEG no signal** (:math:`\mu V`)
Signal detection criterion for EEG channels.
-**EOG no signal (:math:`\mu`V)** EQUATION PROBLEM - MATH DOES NOT APPEAR TO WORK WHEN BOLD???
+**EOG no signal** (:math:`\mu V`)
Signal detection criterion for EOG channels.
@@ -1828,15 +1830,16 @@ marks. The case of the keywords in the file does not matter. The
ending ``.ave`` is suggested for the average description
files.
-The general format of the description file is:
+The general format of the description file is::
-``average {``
- <*common parameters*>
-``category {``
- <*category definition parameters*>
-``}``
-
-... ``}``
+ average {
+ <common parameters>
+ category {
+ <category definition parameters>
+ }
+
+ ...
+ }
The file may contain arbitrarily many categories. The word ``category`` interchangeable
with ``condition`` .
@@ -2103,15 +2106,15 @@ marks. The case of the keywords in the file does not matter. The
ending ``.cov`` is suggested for the covariance-matrix
description files.
-The general format of the description file is:
-
-``cov {``
- <*common parameters*>
-``def {``
- <*covariance definition parameters*>
-``}``
+The general format of the description file is::
-... ``}``
+ cov {
+ <*common parameters*>
+ def {
+ <*covariance definition parameters*>
+ }
+ ...
+ }
The file may contain arbitrarily many covariance definitions,
starting with ``def`` .
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
index b5ab5c8..33d8189 100755
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -1082,15 +1082,15 @@ The command-line options are:
**\---src <*name*>**
The source space to be listed. This can be either the output from mne_make_source_space
- (*src.fif), output from the forward calculation (*fwd.fif), or
- the output from the inverse operator decomposition (*inv.fif).
+ (`*src.fif`), output from the forward calculation (`*fwd.fif`), or
+ the output from the inverse operator decomposition (`*inv.fif`).
**\---mri <*name*>**
A file containing the transformation between the head and MRI coordinates
is specified with this option. This file can be either a Neuromag
- MRI description file, the output from the forward calculation (*fwd.fif),
- or the output from the inverse operator decomposition (*inv.fif).
+ MRI description file, the output from the forward calculation (`*fwd.fif`),
+ or the output from the inverse operator decomposition (`*inv.fif`).
If this file is included, the output will be in head coordinates.
Otherwise the source space will be listed in MRI coordinates.
@@ -1618,7 +1618,7 @@ by mne_convert_mne_data are:
**\---tag <*name*>**
By default, all variables in the matlab output files start with
- MNE_. This option allows to change this prefix to <*name*> _.
+ ``mne\_``. This option allows to change this prefix to <*name*> _.
**\---meg**
@@ -1666,27 +1666,58 @@ by mne_convert_mne_data are:
Guide to combining options
==========================
-The combination of options is quite complicated. The :ref:`BEHDCIII` should be helpful to determine the combination
-of options appropriate for your needs.
+The combination of options is quite complicated. The :ref:`BEHDCIII` should be
+helpful to determine the combination of options appropriate for your needs.
.. _BEHDCIII:
.. table:: Guide to combining mne_convert_mne_data options.
- ============================================ ======== ===================================================================================== ===============================
- Desired output Format Required options Optional options
- ============================================ ======== ===================================================================================== ===============================
- forward model fif --fwd <*name*> --out <*name*> --meg and/or --eeg --fif --bad <*name*> --surfsrc
- forward model mat --fwd <*name*> --out <*name*> --meg and/or --eeg --bad <*name*> --surfsrc
- forward model and sensor covariance mat --fwd <*name*> --out <*name*> --senscov <*name*> --meg and/or --eeg --bad <*name*> --surfsrc
- sensor covariance fif --fwd <*name*> --out <*name*> --senscov <*name*> --noiseonly --fif --meg and/or --eeg --bad <*name*>
- sensor covariance mat --senscov <*name*> --out <*name --bad <*name*>
- sensor covariance eigenvalues text --senscov <*name*> --out <*name --eig --bad <*name*>
- evoked MEG/EEG data mat --meas <*name*> --out <*name --sel <*name*> --set <*number*>
- evoked MEG/EEG data forward model mat --meas <*name*> --fwd <*name*> --out <*name*> --bad <*name*> --set <*number*>
- inverse operator data mat --inv <*name*> --out <*name
- inverse operator data evoked MEG/EEG data mat --inv <*name*> --meas <*name*> --out <*name
- ============================================ ======== ===================================================================================== ===============================
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | Desired output | Format | Required options | Optional options |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | forward model | fif | | \---fwd <*name*> | \---bad <*name*> |
+ | | | | \---out <*name*> | \---surfsrc |
+ | | | | \---meg and/or \---eeg | |
+ | | | | \---fif | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | forward model | mat | | \---fwd <*name*> | \---bad <*name*> |
+ | | | | \---out <*name*> | \---surfsrc |
+ | | | | \---meg and/or --eeg | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | forward model and sensor covariance | mat | | \---fwd <*name*> | \---bad <*name*> |
+ | | | | \---out <*name*> | \---surfsrc |
+ | | | | \---senscov <*name*> | |
+ | | | | \---meg and/or --eeg | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | sensor covariance | fif | | \---fwd <*name*> | \---bad <*name*> |
+ | | | | \---out <*name*> | |
+ | | | | \---senscov <*name*> | |
+ | | | | \---noiseonly | |
+ | | | | \---fif | |
+ | | | | \---meg and/or --eeg | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | sensor covariance | mat | | \---senscov <*name*> | \---bad <*name*> |
+ | | | | \---out <*name*> | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | sensor covariance eigenvalues | text | | \---senscov <*name*> | \---bad <*name*> |
+ | | | | \---out <*name*> | |
+ | | | | \---eig | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | evoked MEG/EEG data | mat | | \---meas <*name*> | \---sel <*name*> |
+ | | | | \---out <*name*> | \---set <*number*> |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | evoked MEG/EEG data forward model | mat | | \---meas <*name*> | \---bad <*name*> |
+ | | | | \---fwd <*name*> | \---set <*number*> |
+ | | | | \---out <*name*> | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | inverse operator data | mat | | \---inv <*name*> | |
+ | | | | \---out <*name*> | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
+ | inverse operator data evoked | mat | | \–--inv <*name*> | |
+ | MEG/EEG data | | | \–--meas <*name*> | |
+ | | | | \–--out <*name*> | |
+ +-------------------------------------+---------+--------------------------+-----------------------+
Matlab data structures
======================
@@ -1720,7 +1751,7 @@ The symbols employed in variable size descriptions are:
.. _BEHCICCA:
-.. table:: Matlab structures produced by mne_convert_mne_data . The prefix given with the ``--tag`` option is indicated <*tag*> , see :ref:`BEHCICCF`. Its default value is MNE.
+.. table:: Matlab structures produced by mne_convert_mne_data.
=============== =======================================
Structure Contents
@@ -1731,6 +1762,8 @@ The symbols employed in variable size descriptions are:
<*tag*> _noise A standalone noise-covariance matrix
=============== =======================================
+The prefix given with the ``--tag`` option is indicated <*tag*> , see :ref:`BEHCICCF`. Its default value is MNE.
+
.. _BABCBIGF:
.. table:: The fields of Matlab structures.
@@ -1816,7 +1849,7 @@ following command-line options:
**\---tag <*tag*>**
By default, all Matlab variables included in the output file start
- with MNE_. This option changes the prefix to <*tag*> _.
+ with ``mne\_``. This option changes the prefix to <*tag*> _.
Matlab data structures
======================
@@ -1916,7 +1949,7 @@ the following command-line options are:
**\---tag <*tag*>**
By default, all Matlab variables included in the description file
- start with MNE_. This option changes the prefix to <*tag*> _.
+ start with ``mne\_``. This option changes the prefix to <*tag*> _.
**\---events <*name*>**
@@ -2027,11 +2060,11 @@ the following command-line options are:
If the ``--inv`` option is present, ``--proj`` has
no effect.
-.. note:: Baseline has not been subtracted from the epochs. This has to be done in subsequent processing with Matlab if so desired.
+.. note:: Baseline has not been subtracted from the epochs. This has to be done in subsequent processing with Matlab if so desired.
-.. note:: Strictly speaking, trigger mask value zero would mean that all trigger inputs are ignored. However, for convenience, setting the mask to zero or not setting it at all has the same effect as 0xFFFFFFFF, *i.e.*, all bits set.
+.. note:: Strictly speaking, trigger mask value zero would mean that all trigger inputs are ignored. However, for convenience, setting the mask to zero or not setting it at all has the same effect as 0xFFFFFFFF, *i.e.*, all bits set.
-.. note:: The digital trigger channel can also be set with the MNE_TRIGGER_CH_NAME environment variable. Underscores in the variable value will *not* be replaced with spaces by mne_browse_raw or mne_process_raw . Using the ``--digtrig`` option supersedes the MNE_TRIGGER_CH_NAME environment variable.
+.. note:: The digital trigger channel can also be set with the MNE_TRIGGER_CH_NAME environment variable. Underscores in the variable value will *not* be replaced with spaces by mne_browse_raw or mne_process_raw . Using the ``--digtrig`` option supersedes the MNE_TRIGGER_CH_NAME environment variable.
.. note:: The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK environment variable. Using the ``--digtrigmask`` option supersedes the MNE_TRIGGER_CH_MASK environment variable.
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
index e204c22..fa9b341 100755
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -196,7 +196,7 @@ The script accepts the following options:
.. table:: Recommended subdivisions of an icosahedron and an octahedron for the creation of source spaces. The approximate source spacing and corresponding surface area have been calculated assuming a 1000-cm2 surface area per hemisphere.
========== ======================== ===================== ===============================
- <*number*> Sources per hemisphere Source spacing / mm Surface area per source / mm2
+ <*number*> Sources per hemisphere Source spacing / mm Surface area per source / mm2
========== ======================== ===================== ===============================
-5 1026 9.9 97
4 2562 6.2 39
@@ -858,7 +858,7 @@ ways:
data used for this purpose should be free of technical artifacts
and epileptic activity of interest. The length of the data segment
employed should be at least 20 seconds. One can also use a long
- (*> 200 s) segment of data with epileptic spikes present provided
+ (`*> 200 s`) segment of data with epileptic spikes present provided
that the spikes occur infrequently and that the segment is apparently
stationary with respect to background brain activity.
@@ -1009,7 +1009,7 @@ the following options:
Save the inverse operator decomposition here. By default, the script looks
for a file whose name is derived from the forward solution file by
replacing its ending ``-fwd.fif`` by <*options*> ``-inv.fif`` , where
- <*options*> includes options ``--meg``, ``--eeg``, and ``--fixed`` with the double
+ <*options*> includes options ``--meg``, ``--eeg``, and ``--fixed`` with the double
dashes replaced by single ones.
**\---destdir <*directory*>**
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index 35860fd..e0705ce 100755
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -172,22 +172,43 @@ and
.. note:: This section does not discuss the transformation between the MRI voxel indices and the different MRI coordinates. However, it is important to note that in FreeSurfer, MNE, as well as in Neuromag software an integer voxel coordinate corresponds to the location of the center of a voxel. Detailed information on the FreeSurfer MRI systems can be found at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems.
-.. _CHDJDEDJ:
.. tabularcolumns:: |p{0.2\linewidth}|p{0.3\linewidth}||p{0.5\linewidth}|
+.. _CHDJDEDJ:
.. table:: Coordinate transformations in FreeSurfer and MNE software packages. The symbols INLINE_EQUATION are defined in :ref:`CHDFFJIJ` Note: mne_make_cor_set /mne_setup_mri prior to release 2.6 did not include transformations INLINE_EQUATION, INLINE_EQUATION, INLINE_EQUATION, and INLINE_EQUATION in the fif files produced.).
- ================== =============================== =======================================================================================================================================
- Transformation FreeSurfer MNE
- ================== =============================== =======================================================================================================================================
- INLINE_EQUATION Not present Measurement data files Forward solution files (*fwd.fif) Inverse operator files (*inv.fif)
- INLINE_EQUATION Not present Channel information in files containing INLINE_EQUATION.
- INLINE_EQUATION Not present MRI description files Separate coordinate transformation files saved from mne_analyze Forward solution files Inverse operator files
- INLINE_EQUATION mri/*mgz files MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
- INLINE_EQUATION mri/transforms/talairach.xfm MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
- INLINE_EQUATION Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
- INLINE_EQUATION Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
- ================== =============================== =======================================================================================================================================
+ +------------------------------+-------------------------------+--------------------------------------+
+ | Transformation | FreeSurfer | MNE |
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_1` | Not present | | Measurement data files |
+ | | | | Forward solution files (`*fwd.fif`)|
+ | | | | Inverse operator files (`*inv.fif`)|
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_{s_1}\dots T_{s_n}` | Not present | Channel information in files |
+ | | | containing :math:`T_1`. |
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_2` | Not present | | MRI description files Separate |
+ | | | | coordinate transformation files |
+ | | | | saved from mne_analyze |
+ | | | | Forward solution files |
+ | | | | Inverse operator files |
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_3` | `mri/*mgz` files | MRI description files saved with |
+ | | | mne_make_cor_set if the input is in |
+ | | | mgz or mgh format. |
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_4` | mri/transforms/talairach.xfm | MRI description files saved with |
+ | | | mne_make_cor_set if the input is in |
+ | | | mgz or mgh format. |
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_-` | Hardcoded in software | MRI description files saved with |
+ | | | mne_make_cor_set if the input is in |
+ | | | mgz or mgh format. |
+ +------------------------------+-------------------------------+--------------------------------------+
+ | :math:`T_+` | Hardcoded in software | MRI description files saved with |
+ | | | mne_make_cor_set if the input is in |
+ | | | mgz or mgh format. |
+ +------------------------------+-------------------------------+--------------------------------------+
.. _BJEBIBAI:
@@ -524,9 +545,16 @@ Tessellation file format
The format of the text format surface files is the following:
- <*nvert*> <*vertex 1*> <*vertex 2*>
-... <*vertex nvert*> <*ntri*> <*triangle 1*> <*triangle 2*>
-... <*triangle ntri*> ,
+ | <*nvert*>
+ | <*vertex 1*>
+ | <*vertex 2*>
+ | ...
+ | <*vertex nvert*>
+ | <*ntri*>
+ | <*triangle 1*>
+ | <*triangle 2*>
+ | ...
+ | <*triangle ntri*> ,
where <*nvert*> and <*ntri*> are
the number of vertices and number of triangles in the tessellation,
@@ -692,9 +720,8 @@ geometry.
The output of each SQUID sensor is a weighted sum of the
magnetic fluxes threading the loops comprising the detection coil.
Since the flux threading a coil loop is an integral of the magnetic
-field component normal to the coil plane, the output of the *k*th
-MEG channel, INLINE_EQUATION, can be approximated
-by:
+field component normal to the coil plane, the output of the `*k*th`
+MEG channel, INLINE_EQUATION, can be approximated by:
.. math:: b_k = \sum_{p = 1}^{N_k} {w_{kp} B(r_{kp}) \cdot n_{kp}}
@@ -764,9 +791,9 @@ The columns of the tables contain the following data:
.. note:: The coil geometry information is stored in the file $MNE_ROOT/share/mne/coil_def.dat, which is automatically created by the utility mne_list_coil_def , see :ref:`BJEHHJIJ`.
-.. _BGBBHGEC:
.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.3\linewidth}|p{0.2\linewidth}|
+.. _BGBBHGEC:
.. table:: Normal coil descriptions. Note: If a plus-minus sign occurs in several coordinates, all possible combinations have to be included.
======= ================================================================ ==== =============================================================== ===============================================================
@@ -792,11 +819,11 @@ The columns of the tables contain the following data:
6001 MIT KIT system axial gradiometer 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
======= ================================================================ ==== =============================================================== ===============================================================
-.. _CHDBDFJE:
.. XXX : incomplete
.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.25\linewidth}|p{0.2\linewidth}|
+.. _CHDBDFJE:
.. table:: Accurate coil descriptions
+------+-------------------------+----+----------------------------------+----------------------+
diff --git a/doc/source/mne-python.rst b/doc/source/mne-python.rst
index cd13ea0..ca0b269 100755
--- a/doc/source/mne-python.rst
+++ b/doc/source/mne-python.rst
@@ -8,5 +8,6 @@ MNE with Python
:maxdepth: 2
getting_started.rst
+ getting_started_at_martinos.rst
auto_examples/index.rst
diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst
deleted file mode 100755
index 9b6b3e7..0000000
--- a/doc/source/tutorial.rst
+++ /dev/null
@@ -1,100 +0,0 @@
-.. _example_config:
-
-=====================================
-Getting started with MNE command line
-=====================================
-
-The quick start guide shows how to run a standard processing of the
-sample data set provided with MNE. XXX add link to data set download
-
-First define your subject::
-
- export SUBJECT=sample
-
-Build your source space::
-
- # MRI (this is not really needed for anything)
- mne_setup_mri --overwrite
-
- # Source space
- mne_setup_source_space --ico -6 --overwrite
-
-Prepare for forward computation::
-
- # For homegenious volume conductor
- mne_setup_forward_model --homog --surf --ico 4
-
- # or for XXX
- mne_setup_forward_model --surf --ico 4
-
-List your bad channels in a file. Example sample_bads.bad contains::
-
- MEG 2443
- EEG 053
-
-Mark bad channels::
-
- mne_mark_bad_channels --bad sample_bads.bad sample_audvis_raw.fif
-
-Compute averaging::
-
- mne_process_raw --raw sample_audvis_raw.fif --lowpass 40 --projoff \
- --saveavetag -ave --ave audvis.ave
-
-Compute the noise covariance matrix::
-
- mne_process_raw --raw sample_audvis_raw.fif --lowpass 40 --projoff \
- --savecovtag -cov --cov audvis.cov
-
-Compute forward solution a.k.a. lead field::
-
- # for MEG only
- mne_do_forward_solution --mindist 5 --spacing oct-6 \
- --meas sample_audvis_raw.fif --bem sample-5120 --megonly --overwrite \
- --fwd sample_audvis-meg-oct-6-fwd.fif
-
- # for EEG only
- mne_do_forward_solution --mindist 5 --spacing oct-6 \
- --meas sample_audvis_raw.fif --bem sample-5120-5120-5120 --eegonly \
- --fwd sample_audvis-eeg-oct-6-fwd.fif
-
- # for both EEG and MEG
- mne_do_forward_solution --mindist 5 --spacing oct-6 \
- --meas sample_audvis_raw.fif --bem sample-5120-5120-5120 \
- --fwd sample_audvis-meg-eeg-oct-6-fwd.fif
-
-Compute MNE inverse operators::
-
- # Note: The MEG/EEG forward solution could be used for all
- mne_do_inverse_operator --fwd sample_audvis-meg-oct-6-fwd.fif \
- --depth --loose 0.2 --meg
-
- mne_do_inverse_operator --fwd sample_audvis-eeg-oct-6-fwd.fif \
- --depth --loose 0.2 --eeg
-
- mne_do_inverse_operator --fwd sample_audvis-meg-eeg-oct-6-fwd.fif \
- --depth --loose 0.2 --eeg --meg
-
-Produce stc files (activation files)::
-
- # for MEG
- mne_make_movie --inv sample_audvis-meg-oct-6-${mod}-inv.fif \
- --meas sample_audvis-ave.fif \
- --tmin 0 --tmax 250 --tstep 10 --spm \
- --smooth 5 --bmin -100 --bmax 0 --stc sample_audvis-meg
-
- # for EEG
- mne_make_movie --inv sample_audvis-eeg-oct-6-${mod}-inv.fif \
- --meas sample_audvis-ave.fif \
- --tmin 0 --tmax 250 --tstep 10 --spm \
- --smooth 5 --bmin -100 --bmax 0 --stc sample_audvis-eeg
-
- # for MEG and EEG combined
- mne_make_movie --inv sample_audvis-meg-eeg-oct-6-${mod}-inv.fif \
- --meas sample_audvis-ave.fif \
- --tmin 0 --tmax 250 --tstep 10 --spm \
- --smooth 5 --bmin -100 --bmax 0 --stc sample_audvis-meg-eeg
-
-And, we're done!
-
-You can now get started with the `examples <auto_examples/index.html>`_.
diff --git a/examples/stats/plot_cluster_1samp_test_time_frequency.py b/examples/stats/plot_cluster_1samp_test_time_frequency.py
index 5503881..69349a1 100755
--- a/examples/stats/plot_cluster_1samp_test_time_frequency.py
+++ b/examples/stats/plot_cluster_1samp_test_time_frequency.py
@@ -8,11 +8,12 @@ in time-frequency power estimates. It uses a non-parametric
statistical procedure based on permutations and cluster
level statistics.
-The procedure consists in :
-- extracting epochs
-- compute single trial power estimates
-- baseline line correct the power estimates (power ratios)
-- compute stats to see if ratio deviates from 1.
+The procedure consists in:
+
+ - extracting epochs
+ - compute single trial power estimates
+ - baseline line correct the power estimates (power ratios)
+ - compute stats to see if ratio deviates from 1.
"""
# Authors: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
diff --git a/examples/stats/plot_cluster_stats_time_frequency.py b/examples/stats/plot_cluster_stats_time_frequency.py
index f9a6d30..15ba184 100755
--- a/examples/stats/plot_cluster_stats_time_frequency.py
+++ b/examples/stats/plot_cluster_stats_time_frequency.py
@@ -8,12 +8,13 @@ power estimates between conditions. It uses a non-parametric
statistical procedure based on permutations and cluster
level statistics.
-The procedure consists in :
-- extracting epochs for 2 conditions
-- compute single trial power estimates
-- baseline line correct the power estimates (power ratios)
-- compute stats to see if the power estimates are significantly different
- between conditions.
+The procedure consists in:
+
+ - extracting epochs for 2 conditions
+ - compute single trial power estimates
+ - baseline line correct the power estimates (power ratios)
+ - compute stats to see if the power estimates are significantly different
+ between conditions.
"""
# Authors: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
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