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...
>
>> 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?
>
>> 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?
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