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Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform with the lh.white surface? Therefore, if I wanted to extract the mean FA for each parcel I would use this newly created volume and the annotation file? I had previously used mri_segstats, but that wouldn't work here. Is that right?
Cheers, Steph
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday, December 09, 2018 4:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
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Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers Bruce
On Sun, 9 Dec 2018, Winkelbeiner, Stephanie A wrote:
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Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file ‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
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