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| and | '''freesurfer_4.3.0''' |
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The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces. After this step, you should realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set). The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual], [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers reading papers], and [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup discussions] with more experienced researchers. |
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| SUBJECTS_DIR='</myMRIdirectory/>' | SUBJECTS_DIR='</myMRIdirectory/>' # root directory for MRI data |
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| for SUBJECT in Subject1 Subject2Subject3 # use your subject names here | for SUBJECT in Subject1 Subject2 Subject3 # use your list of subject names here |
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| cd ${SUBJECTS_DIR} |
# creates surfaces necessary for BEM head models |
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rm $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf rm $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf rm $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf rm $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf |
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| # creates fiff-files for MNE describing MRI data | |
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| # create a source space from the cortical surface created in Freesurfer | |
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mri_convert -ot cor $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz $SUBJECTS_DIR/$SUBJECT/mri/T1/ mkheadsurf -subjid $SUBJECT |
Head Model and Source Space Creation in MNE
Make sure you've typed
mne_setup_2.6.0
freesurfer_4.3.0
setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces.
After this step, you should realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set).
The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual], [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers reading papers], and [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup discussions] with more experienced researchers.
SUBJECTS_DIR='</myMRIdirectory/>' # root directory for MRI data
for SUBJECT in Subject1 Subject2 Subject3 # use your list of subject names here
do
# creates surfaces necessary for BEM head models
mne_watershed_bem --overwrite --subject $SUBJECT
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_inner_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skin_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_brain_surface' $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf
# creates fiff-files for MNE describing MRI data
mne_setup_mri --overwrite --subject $SUBJECT
# create a source space from the cortical surface created in Freesurfer
mne_setup_source_space --spacing 5 --overwrite --subject $SUBJECT
done