Dear Surfer experts,
(Most likely Dough)
It is common practice to perform the slice time correction first and than the motion correction. However free surfer seems to work in the opposite way.
I have tried to write a mini matlab freesurfer script for the common way.
system(['stc-sess -s ' funcdir(i).name ' -i f -o fstc -so siemens'])
system(['mc-sess -s ' funcdir(i).name ' -fstem fstc -fmcstem fstcmc -per-run'])
This seems to work.
My problem is how do I get the resulting fstcmc.ni.gz on to the fsaverage surface using spherical alignment?
Jan
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