[med-svn] [python-mne] 229/376: DOC : some cleanup in index page
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:52 UTC 2015
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yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 88fc40af222b40b92f90e07f9e626c30a9b42d3f
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Tue May 3 10:29:31 2011 -0400
DOC : some cleanup in index page
---
doc/source/command_line_tutorial.rst | 100 +++++++++++++++++++++++++++++++++++
doc/source/conf.py | 3 ++
doc/source/index.rst | 36 ++++++-------
doc/source/manual.rst | 27 ++++++++++
doc/source/mne-python.rst | 2 +-
5 files changed, 146 insertions(+), 22 deletions(-)
diff --git a/doc/source/command_line_tutorial.rst b/doc/source/command_line_tutorial.rst
new file mode 100644
index 0000000..b6448bf
--- /dev/null
+++ b/doc/source/command_line_tutorial.rst
@@ -0,0 +1,100 @@
+.. _example_command_line:
+
+=====================================
+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 Python `examples <auto_examples/index.html>`_.
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 43cedde..56404d2 100755
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -220,3 +220,6 @@ latex_logo = "_static/logo.png"
# If false, no module index is generated.
latex_use_modindex = True
+
+
+trim_doctests_flags = True
\ No newline at end of file
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 53355ab..7e3f16d 100755
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -9,31 +9,25 @@ 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>`_
-Manual:
+Manual
+======
.. toctree::
- :maxdepth: 1
-
- manual/intro
- manual/list
- manual/cookbook
- manual/browse
- manual/forward
- manual/mne
- manual/analyze
- manual/morph
- manual/convert
- manual/matlab
- manual/utilities
- manual/sampledata
- manual/reading
- manual/AppA
- manual/AppB
- manual/AppInstall
- manual/AppReleaseNotes
- manual/AppEULA
+ :maxdepth: 2
+
+ manual
+
+MNE with Python
+===============
+
+.. toctree::
+ :maxdepth: 2
+
mne-python
* :ref:`search`
diff --git a/doc/source/manual.rst b/doc/source/manual.rst
new file mode 100644
index 0000000..2f063e5
--- /dev/null
+++ b/doc/source/manual.rst
@@ -0,0 +1,27 @@
+.. _manual:
+
+Manual
+======
+
+.. toctree::
+ :maxdepth: 1
+
+ manual/intro
+ manual/list
+ manual/cookbook
+ manual/browse
+ manual/forward
+ manual/mne
+ manual/analyze
+ manual/morph
+ manual/convert
+ manual/matlab
+ manual/utilities
+ manual/sampledata
+ manual/reading
+ manual/AppA
+ manual/AppB
+ manual/AppInstall
+ manual/AppReleaseNotes
+ manual/AppEULA
+
diff --git a/doc/source/mne-python.rst b/doc/source/mne-python.rst
index 79d0ab7..cd13ea0 100755
--- a/doc/source/mne-python.rst
+++ b/doc/source/mne-python.rst
@@ -1,4 +1,4 @@
-.. _documentation:
+.. _mne_python:
======================
MNE with Python
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