Resample CAT12 outputs to fsaverage

1

Hi,

I try to resample cat12 cortical thickness outputs to fsaverage. When using mri_surf2surf it fails not having a label file of the source. I am not sure how to address that being a novice in terms of surface analyses and not sure where I get this information from. Can somebody provide me with some hints how to achieve the resampling?

Grateful for any input.

Cheers,
Marvin

Command

mri_surf2surf --srcsubject sub-000480a3 --trgsubject fsaverage7 --surfreg sphere.reg.T1.gii --hemi rh --sval sub-000480a3/surf/rh.thickness.T1 --tval sub-000480a3/surf/rh.fsaverage.thickness.T1.gii --cortex 

sysname  Linux
hostname node072
machine  x86_64
user     fatx405
srcsubject = sub-000480a3
srcval     = sub-000480a3/surf/rh.thickness.T1
srctype    = 
trgsubject = fsaverage7
trgval     = sub-000480a3/surf/rh.fsaverage.thickness.T1.gii
trgtype    = 
srcsurfreg = sphere.reg.T1.gii
trgsurfreg = sphere.reg.T1.gii
srchemi    = rh
trghemi    = rh
frame      = 0
fwhm-in    = 0
fwhm-out   = 0
label-src  = rh.cortex.label
label-trg  = rh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg /scratch/fatx405.1558254/sub-000480a3/tmp//input/sub-000480a3/surf/rh.sphere.reg.T1.gii
Loading source data
Reading source subject label mask rh.cortex.label
error: No such file or directory
error: mri_surf2surf: could not open label file /scratch/fatx405.1558254/sub-000480a3/tmp//input/sub-000480a3/label/rh.cortex.label

CAT12 output

lh.central.T1.gii     rh.pbt.T1
lh.pbt.T1             rh.pial.T1.gii
lh.sphere.reg.T1.gii  rh.sphere.reg.T1.gii
lh.sphere.T1.gii      rh.sphere.T1.gii
lh.thickness.T1       rh.thickness.T1
rh.central.T1.gii     rh.white.T1.gii
2

Issue is solved using the builtin resampling functionality of cat12. Example code called within the cat container (Małgorzata Wierzba / cat-container · GitLab) is cat_standalone.sh -b $CAT_CODE_DIR/cat_standalone_resample.txt -a1 "12" -a2 "0" /tmp_out/lh.thickness.T1

3

Hello, i am also tring to resample the cat12 cortical thickness into freesurfer space (fsaverage) and convert these files into mgh files that could be processed using Freesurfer. Currently, i used the resample-smooth function within cat12 and got these smoothed thickness within freesurfer space for each subject: lh.central.sub-023_T1_bias_corrected.gii; lh.central.sub-023_T1_bias_corrected.dat. May I ask did you convert these files into freesurfer compatible files？ Thanks a lot!