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