yes, those commands look right, except I think you don't need to specify 
 --surfreg my_avg_subject.sphere.reg 

It will automatically do this for you
On 2/19/2020 1:44 PM, Marina Fernández wrote:

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Hi experts,

I am running the following command to create de average subjecto with Freesurfer v6.0:

             make_average_subject --out my_avg_subject --fsgd  fsgd.txt

Then, I want to do surface analysis with the thickness of each subject projected onto my_avg_subject. I would like to know if it is correct to run these commands  before that statistical analysis:

             surfreg --s s_001 --t  my_avg_subject --o  my_avg_subject.sphere.reg

             mris_preproc --fsgd nfsgd.txt --target my_avg_subject  --surfreg my_avg_subject.sphere.reg --meas thickness --srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh 

Finally, I would use "[l/r]h.fsgd.mgh" file to do the thickness surface analysis.

Is it correct? Should I run surfreg and use the output in mris_preproc?
What is the advantage?

Thank you very much!
Marina-

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