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Thanks for your reply Doug,
Just to clarify
1) To do this, I would first run mris_preproc with the early onset (on to the left hemisphere)
mris_preproc --target fsaverage_sym --hemi lh --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out lh.subject.sm00.mgh --s subj_06_1 --s subj_08_1 --s subj_02_1/xhemi --s subj_04_1/xhemi
the subject/xhemi are subjects with the early onset on the right hemisphere surf register to the left
then I would run mris_preproc with the late onset side (on to the right hemisphere, but reg to the right)
mris_preproc --target fsaverage_sym --hemi lh --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out rh.subjects.sm00.mgh --s subj_06_1/xhemi --s subj_08_1/xhemi --s subj_02_1 --s subj_04_1
then I would run
mri_concat lh.subject.sm00.mgh rh.subjects.sm00.mgh --o subjects.sm00.mgh --paired-diff
and then proceed to the rest of the steps on the xhemi wiki tutorial. Is this correct?
2) For the LME, How do I create a stack of xhemi thickness and volume differences with longitudinal time points? following the LME tutorial,
mris_preproc --qdec-long qdec.table.dat --target fsaverage_sym --hemi lh --meas thickness --out lh.thickness.mgh
do I just do the same as above? how do I get it to use the xhemi subjects?
Sincerely, Xiaoyu Wang
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, April 19, 2019 12:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] xhemi Longitudinal Comparison
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On 4/19/2019 11:35 AM, Wang, Xiaoyu wrote:
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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.
Not sure what you mean. If you ran mri_concat with --paired-diff, then you would have a stack of cross-hemi differnce maps, then you would just use the standard group analysis to compare healthy vs patient or look at age effect, etc.
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?
In principle you could use LME. You would just feed it the stack of thickness or volume differences.
Sincerely,
Xiaoyu Wang
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