Hello,
I am trying to convert a w file into a label file, and the best way I came up with seems like it is too complicated to be the actual best way.
What I am doing below is reading a list of subjects, and then for each subject, 1.) running mri_surfcluster, 2.) merging its output into a new label, and 3.) removing the component labels that went into it.
# entered in bash shell # generate the .w file paint-sess -sf Subject_Lists/bw-group-error-5 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh # merge labels cat Subject_Lists/bw-group-error-5 | while read subject; do mri_surfcluster --in $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-lh.w --thmin 0.5 --sign pos --subject $subject --hemi lh --surf orig --annot aparc --minarea 1 --sum $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-h-label.sum --olab $subject/label/rACC_lh_pos_0_ASce68 ; cd $subject/label; mri_mergelabels $(ls rACC_lh_pos_0_ASce68*.label | sed 's/rACC/-i rACC/g') -o rACC_lh_pos_0_ASce68.label; rm rACC_lh_pos_0_ASce68-0*.label; cd $SUBJECTS_DIR; done #check in tksurfer surf-sess -s mano001 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh -fthresh 1
It seems to work, but if there is a more direct way, it may be better just because there is potential room for error the way I am doing it.
Thanks, Rob