Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@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
External Email. Use Caution.
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:
External Email - Use Caution
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: swinkel...@northwell.edu
Northwell Health
Visit us at Northwell.edu
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