Hello FreeSurfers,<div><br></div><div>I want to compare cortical thickness differences between my two groups.  Is this the correct pipeline?</div><div><br></div><div>I ran make_average_subject on each group.</div><div><br>

</div><div>To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh</div>

<div><br></div><div>And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh.  Is this the right way to do this?  mris_thickness_diff says it should only be used on the same subject.  mris_diff says it is still being tested.  I also see mris_thickness_comparison.  Which command is the best to use to get a thickness difference map?</div>

<div><br></div><div>Thank you very much,<br>Jeff Sadino</div>