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# 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
and
setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
SUBJECTS_DIR='</myMRIdirectory/>' for SUBJECT in Subject1 Subject2Subject3 # use your subject names here do cd ${SUBJECTS_DIR} # 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