The way that mris_preproc used to work was confusing. It made it look like you were actually sampling to my_subject_average. In reality, it was only using my_subject_average to perform smoothing -- the entire analysis was done in fsaverage space. To clarify this, I required that there by a new surface registration file when something other than fsaverage is specified as the target. If you want to perform the analysis in my_subject_average, then run the surfreg script for each subject targeting my_subject_average. If you want to do it as before, then use fsaverage. You can visualize the results on my_subject_average.

Dear FreeSurfer experts,

I am using mris_preproc command with following options:

     mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average --hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file

I observe mris_preproc uses mri_surf2surf. My question is related to Freesurfer version. Using FreeSurfer 5.3, mri_surf2surf takes sphere.reg as srcsurfreg, while with Freesurfer 6 script mri_surf2surf has changed. It takes my_subject_average.sphere.reg (target of mris_preproc) as srcsurfreg. I get an error because my_subject_average.sphere.reg file doesn't exist inside s_001 folder. 

Why Freesurfer 6 changes srcsurfreg to $target.sphere.reg? What can I do in order to be coherent with my script which was designed using Freesurfer 5.3?

Thanks in advance,

M del Mar

  

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