Resample surf.gii (fmriprep output) from fsnative to fsaverage

Software Support
1

Dear experts,

I am seeking help on resampling the anat/midthickness.surf.gii file from fsnative space to fsaverage space. Currently, I have functional outputs in both fsaverage and fsaverage5 spaces. The midthickness.surf.gii file in fsaverage space is essential for the smoothing.

It appears that desc-reg_sphere.surf.gii is the registration file for fsaverage, while sphere.surf.gii is the sphere surface. Could you please advise me on how to proceed with this resampling?

Thank you!
Yijun

2

Hi @yijun,

Try:

mri_surf2surf \
--srcsubject $SUBJECT \
--srcsurfval $METRIC.surf.gii \
--trgsubject fsaverage \
--trgsurfval $OUTPUTNAME.surf.gii \
--hemi $HEMI

Best,
Steven

3

Thanks for your reply. I tried before, it didn’t work. Please see the error message below:


mri_surf2surf --srcsubject sub-LM002 --srcsurfval /media/dcnladmin/sunset/LM/test/testsurfresample/sub-LM002_ses-T2_hemi-L_midthickness.surf.gii --trgsubject fsaverage --trgsurfval /media/dcnladmin/sunset/LM/test/testsurfresample/test.surf.gii --hemi lh

7.4.1

setenv SUBJECTS_DIR /media/dcnladmin/sunset/LM/test/testsurfresample
cd /media/dcnladmin/sunset/LM/test/testsurfresample
mri_surf2surf --srcsubject sub-LM002 --srcsurfval /media/dcnladmin/sunset/LM/test/testsurfresample/sub-LM002_ses-T2_hemi-L_midthickness.surf.gii --trgsubject fsaverage --trgsurfval /media/dcnladmin/sunset/LM/test/testsurfresample/test.surf.gii --hemi lh 

sysname  Linux
hostname dcnladmin-Super-Server
machine  x86_64
user     dcnladmin
srcsubject = sub-LM002
srcval     = /media/dcnladmin/sunset/LM/test/testsurfresample/sub-LM002_ses-T2_hemi-L_midthickness.surf.gii
srctype    = 
trgsubject = fsaverage
trgval     = /media/dcnladmin/sunset/LM/test/testsurfresample/test.surf.gii
trgtype    = 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
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 /media/dcnladmin/sunset/LM/test/testsurfresample/sub-LM002/surf/lh.sphere.reg
Loading source data
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
MRISreadGiftiAsMRI: no overlay data found in file /media/dcnladmin/sunset/LM/test/testsurfresample/sub-LM002_ses-T2_hemi-L_midthickness.surf.gii
Segmentation fault (core dumped)
5

Hi @Steven ,
the mri_surf2surf only works with metric data, not the surface itself.
hemi-L_thickness.shape.gii <------worked
hemi-L_pial.surf.gii <------didn’t work

Best,
Yijun