Hi Shige, those are fine, but there is a warning here about performing the mri_surf2surf step. You need to make sure that you are doing this properly because it will run and complete even if you are not doing it properly:).
to map the left hemi, run something like: mri_surf2surf --srcsubject subject --srchemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsubject fsaverage_sym --trghemi lh --trgsurfreg sphere.reg --tval lh.subject.yourdata.mgh --sval subject/surf/lh.yourdata.mgh to map the right hemi: mri_surf2surf --srcsubject subject/xhemi --srchemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsubject fsaverage_sym --trghemi lh --trgsurfreg sphere.reg --tval rh.subject.yourdata.mgh --sval subject/surf/rh.yourdata.mgh Note that in the 2nd call, you specify "subject/xhemi" as the subject and still continue to use "lh" eventhough you are mapping the rh. Like I said, it is tricky! doug On 12/06/2012 01:42 PM, Shigetoshi Takaya wrote: > Thanks for your reply, Doug > > After inter-hemispheric registration onto fsaverage_sym using surfreg, I did > not use mris_preproc in my analysis because of the following two reasons: > (i) I thought I can't use "--meas" because the input is an arbitrary surface > data. > (ii) I don't want to use "--paired-diff" because I don't want the input > "pruned" before taking the difference. > > Instead, I took the following steps: > (1) resample the data onto fsaverage_sym using mri_surf2surf > (2) take the difference in each subject using fscalc > $fscalc lh.lh_subj1.mgz -sub lh.rh_subj1.mgz --o lh.lh-rh_subj1.mgz > (3) concatenate the subjects together > $mri_concat lh-rh_subj1 lh-rh_subj2 .... --o > (4) smooth (mris_fwhm) and analyze (mri_glmfit). > > Are these steps not good for mri_glmfit-sim? > > > Best, > Shige > > > -----Original Message----- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Thursday, December 06, 2012 11:59 AM > To: Shigetoshi Takaya > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: mri_glmfit-sim for interhemispheric comparison > > Shige, it is looking for tables of cluster p-values (the csd files). > When you followed the wiki instructions, did you tell it to use > fsaverage_sym as the target subject? You must have used a subject called > "average". > > doug > > > On 12/06/2012 11:53 AM, Shigetoshi Takaya wrote: >> Hi Doug, >> >> I did surface-based inter-hemispheric comparison. >> >> I used an arbitrary surface data (.mgz) resampled from a volume data >> (.nii), otherwise I follow the instruction. >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi >> >> I got a good result for mri_glmfit. But when I run mri_glmfit-sim, the >> following error messeage popped up. >> >> ERROR: cannot find >> >> $FRESURFER_HOME/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/a >> bs/th20/mc-z.csd >> >> I did not find "fwhm00"anywhere in the downloaded file >> "mult-comp-cor", although I found fwhm01-30 directories. Am I missing >> somethine? >> >> Thank you very much in advance, >> >> Shige >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
