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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
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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.External Email - Use Caution
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.mghand 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.
In principle you could use LME. You would just feed it the stack of thickness or volume differences.
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
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