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 88fc40af222b40b92f90e07f9e626c30a9b42d3f Author: Alexandre Gramfort <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
