[Freesurfer] Question about compare left and right hemi of longitudinal data

Hi, all experts. I want to compare changes rate between left and right hemisphere of longitudinal data, How should I do that, how to combine xhemi with two stage or LME? Best, Lanbo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Lanbo, you could look at longitudinal changes of the left-right difference in volume per ROI. Or do you mean on the cortical thickness map (I have never done that, but probably works similarly, construct left -right registration, compute difference, then run the LME on that). Best, Martin

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Thanks for replying me. But I still have two questions. Firstly, when I try xhemi on pre-possessed longitudinal data, it showed error like this: Performing left-right swap of labels TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, 3.72529e-08, 3.35276e-08) j_ras = (-2.6077e-08, -3.72529

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Lanbo, what is the exact command you use for this? The problem is that the script or your command does not pass the right flags to recon all. Whenever recon-all is supposed to work on a longitudinal directory it needs to know the base and the long so the recon all command needs to show -l

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Martin, I didn't try to run recon-all, I try to run flipped. The code I used is: foreach subject (subj_27_2.long.s27_base) foreach? surfreg --s $subject --t fsaverage_sym --lh foreach? surfreg --s $subject --t fsaverage_sym --lh --xhemi foreach? end Thanks, Lanbo On Tue, Jan 16, 2018 at

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Is the problem that the surfreg command is failing or that you don't know how to apply LME? On 1/17/18 9:55 AM, lanbo Wang wrote: Hi Martin, I didn't try to run recon-all, I try to run flipped. The code I used is: foreach subject (subj_27_2.long.s27_base) foreach?   surfreg --s $subject --t f

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

The problem is that the surfreg command is failing. Thanks, Lanbo On Thu, Jan 18, 2018 at 5:14 PM, Douglas Greve wrote: > Is the problem that the surfreg command is failing or that you don't know > how to apply LME? > > On 1/17/18 9:55 AM, lanbo Wang wrote: > > Hi Martin, > > I didn't try to ru

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Lanbo and Doug, What happens is this: surfreg calls xhemireg (these are shell scripts) xhemireg calls "recon-all -sb $subject/xhemi -talairach" recon-all complains, because this $subject is a longitudinal time point. recon-all expects longitudinal time point to be passed as -long inst