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.