Hi FreeSurfer experts,
I have a question about two specific steps in my fc pipeline. Since my seed is
a single vertex, I convert the seed label to a mask, which I then smooth and
binarize, and then convert to a volume file for fcseed-sess.
1) Is there way to directly convert a label into a cortical mask?
Right now I use mri_label2label to create an outmask
mri_label2label -s fsaverage -regmethod -surface -hemi -srclabel
$SUBJECTS_DIR/{subject}/label/{label} -trglabel
$SUBJECTS_DIR/{subject}/label/junk.label -outmask
$SUBJECTS_DIR/{subject}/mri/{mask}
cd $SUBJECTS_DIR/{subject}/label
rm junk.label
Is there a way to do this where I do not have to create another label in order
to make a mask?
2) I can't figure out how to convert a cortical mask to a volume file (that I
can use in fcseed-sess) using stable 5.3. I've tried to use mri_convert to
create a volume file, but fcseed-sess errors out using this vol file (0
segmentations, core segmentation dumped)
The command I use is:
mri_convert $SUBJECTS_DIR/{subject}/mri/{mask}
$SUBJECTS_DIR/{subject}/mri/{mask}.vol.mgz
Currently, if I want to do this I need to switch to stable dev and run
mri_surf2vol:
mri_surf2vol -so $SUBJECTS_DIR/fsaverage1/surf/lh.pial
$SUBJECTS_DIR/{subject}/mri/{mask} -subject fsaverage -o
$SUBJECTS_DIR/{subject}/mri/{mask}.vol.mgz
Is there a way that I can convert a surface mask to a useable volume for
fcseed-sess in stable 5.3, rather than having to switch to stable dev?
Thank you for your help!
Anais Rodriguez-Thompson
Clinical Research Coordinator
Brain Genomics Laboratory
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Phone: (617) 643-3215
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