Re: [Freesurfer] Still confused by group analysis..

On 6/12/13 7:03 AM, Tudor Popescu wrote:

Sorry Doug, wasn't sure whether you'd seen my last reply to this..

On 6 Jun 2013 21:37, "Tudor Popescu" <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:

Thanks Doug,



        So if I want to use the study-specific "average" subject
        surface with mri_surf2surf, rather than the generic
        "fsaverage" one, how can this be done given that the
        required ls.white file only exists in the latter but not
        in the former? Can I just rename (or duplicate) ls.white
        into ls.white_avg?

    You can copy it or create a symbolic link.

So it is OK to copy the required lh.white file from the generic
average subject "fsaverage" and apply mri_surf2surf upon the
study-specific average subject ("average")? It still seems to me
that "average" should have its own (different) lh.white...

Yes it should. Did make_average_subject not create it?

        Shouldn't the input to mri_glmfit be the output of
        mri_surf2surf? In the group tutorial, the former is
        "lh.gender_age.thickness.10.mgh" while the latter is
        "lh.gender_age.thickness.10B.mgh". Or should it just be
        the unsmoothed output of mris_preproc?

    Yes, I can't remember why I put the "B" there, maybe to keep
    people from overwriting  lh.gender_age.thickness.10.mgh during
    the tutorial and having to wait the 10min or so for it to get
    recreated.

But if all these commands transform the same file (output of
mris_preproc becomes input of mri_surf2surf, which then feeds into
mri_glmfit), then why is it still necessary to keep intact the
original lh.gender_age.thickness.10.mgh, when all you need for the
group analysis is the mri_surf2surf'd version?

Sorry, I'm lost here. What are the names of the files?

        Assuming the label files (corresponding to my ROI, and
        extracted from the Destrieux atlas) are different for each
        subject, and given mri_glmfit is called just once, for all
        subjects, which label file (corresponding to what subject)
        should I point it to?

    You need to create the label in the average subject. There is
    a Destrieux atlas there.

Again, by "average subject" do you mean here the generic one
(fsaverage) or the study-specific one (average)? Should the former
be used at any point of a group analysis, if the latter exists?

If you are doing your group analysis on a custom average, then do not use fsaverage at any point. doug