Hi Jeff, make_average_subject is just if you want to visualize results on a surface presenting the average of your own subjects, rather than using the provided 'fsaverage'. It is not necessary (and not related) to performing group statistical comparisons per se.
You can use the 'qdec' utility to do compute maps of groupwise statisical differences on the surface, after first running recon-all with the -qcache flag. cheers, -MH On Mon, 2012-02-13 at 20:06 -1000, Jeff Sadino wrote: > Hello FreeSurfers, > > > I want to compare cortical thickness differences between my two > groups. Is this the correct pipeline? > > > I ran make_average_subject on each group. > > > 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 > > > 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? > > > Thank you very much, > Jeff Sadino > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
