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Dear FreeSurfer Experts,

We are trying to compare the early onset hemisphere vs Late onset hemisphere of PD patients.

I am trying to use Xhemi in order to reorganize all early onset hemisphere to the left hemisphere and the late onset to the right hemisphere.

I am following the Xhemi wiki tutorial as well as the freesurfer archives messages between Doug and Paula with Subject: [Filipping issue] from 2014.

I saw that Doug had told Paula to run mris_preproc twice, first do the left normally

>>> mris_preproc --hemi lh --meas thickness --surfreg
>>> fsaverage_sym.sphere.reg --s subject1 --s subject2 --o
>> subjects.lh.sm00.mgh

 and then run the right hemisphere subjects with --s subject/xhemi in the command line.

>>> mris_preproc --hemi lh --meas thickness --surfreg
>>> fsaverage_sym.sphere.reg --s subject3/xhemi --s subject4/xhemi --o
>>> subjects.rh.sm00.mgh

Then use mri_concat to fuse the two outputs together.

1) My question for this is how do you then compare to the right hemisphere? From the wiki, you need the --xhemi and --paired-diff in the command line to do a cross hemisphere comparison.

the above is great to compare to healthy control, but how do I adapt that to do a cross hemisphere comparison.

2) The question I have is how to do a longitudinal comparison between Left and right hemispheres with the xhemi data. Would it be possible to use xhemi together with Mass-Univariate LME?

If not, do I need to use Xhemi to generate thickness and volume data? Can't I just use the regular stat data from the regular reconstruction?

Sincerely,

Xiaoyu Wang