Diff for "AnalyzingData/MNE_MRI_processing" - Meg Wiki
location: Diff for "AnalyzingData/MNE_MRI_processing"
Differences between revisions 3 and 4
Revision 3 as of 2010-06-09 14:03:20
Size: 1339
Editor: YaaraErez
Comment:
Revision 4 as of 2010-06-09 14:14:28
Size: 1214
Editor: YaaraErez
Comment:
Deletions are marked like this. Additions are marked like this.
Line 21: Line 21:
        # creates surfaces necessary for BEM head models
Line 22: Line 23:

 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
Line 34: Line 29:
        # creates fiff-files for MNE describing MRI data
Line 36: Line 32:
        # create a source space from the cortical surface created in Freesurfer
Line 37: Line 34:

 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

CbuMeg: AnalyzingData/MNE_MRI_processing (last edited 2016-06-28 09:27:42 by OlafHauk)