what version of freesurfer are you running?
On 3/6/2020 10:03 AM, Marina Fernández wrote:
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Dear freesurfer experts, I run the following commands to perform analysis with projected surfaces on my average subject: make_average_subject --out my_avg_subject --fsgd fsgd.txt surfreg --s s_001 --t my_avg_subject --o my_avg_subject.sphere.reg mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness --srcfmt curv --hemi [l/r]h --out [l/r]h.fsgd.mgh Theoretically, the mri_preproc function will automatically use the my_avg_subject.sphere.reg file because I specify my_avg_subject as the target subject. The problem is that in the output that comes out in the terminal while this function is running, it is specified that the file [l/r]h.sphere.reg is selected instead of [l/r]h.my_avg_subject.sphere.reg. Additionally, I did a test specifying the flag "--surfreg my_avg_subject.sphere.reg" in mris_preproc and the values of the output surface are different from the output that I have when I don't specify the flag --surfreg in mris_preproc (so, If I don't specify it, I think that definitely the function doesn't automatically use the file generated in surfreg, I think the default sphere.reg is used). What should I do? Is it better to specify the “--surfreg my_avg_subject.sphere.reg” flag in the mris_preproc function? Thanks in advance. Best regards, Marina.
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