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.
On 11/7/17 8:02 AM, M del Mar Velasco wrote:
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 /s//rcsurfreg/. 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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