I think you need to specify ‘--src_type curv’ and ‘--trg_type curv’ to read thickness files.
It looks like you passed ‘thickness’ to the wrong flag. Use ‘—srcsurfval’ and ‘—trgsurfval’ instead.
Here is wiki help page - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2surf
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sahil Bajaj Sent: Wednesday, December 6, 2023 3:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Faces and vertices error !
External Email - Use Caution Hi FreeSurfer community,
I am trying to map subject-specific cortical thickness map to standard fsaverage space and I ran the following command where sub1_filled is my individual subject in native:
mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject fsaverage --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval fsaverage/surf/lh.thickness
After I run the above command, I am getting the following output and error. I am not sure how to resolve this and whether there is something wrong with my command line or with the data. I would greatly appreciate any help.
Source registration surface changed to thickness
Target registration surface changed to thickness
7.4.1
setenv SUBJECTS_DIR /Users/sbajaj/FS_Projects/
cd /Users/sbajaj/FS_Projects
mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject fsav1 --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval fsav1/surf/lh.thickness
sysname Darwin
hostname MDACM0CL9004107
machine x86_64
user sbajaj
srcsubject = sub1_filled
srcval = sub1/surf/lh.thickness
srctype =
trgsubject = fsav1
trgval = fsav1/surf/lh.thickness
trgtype =
srcsurfreg = thickness
trgsurfreg = thickness
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg /Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness
nquads=4456450, nvertices=341
error: ERROR: MRISread: file '/Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!