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
--
Robert P. Levy, B.A.
Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2656
Charlestown, MA 02129
email: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
