Hi Doug, I think I solved the registration issue. This is my command: mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval bert/surf/lh_av.thickness --trg_type curv
Any objections? Thanks, Michael Begin forwarded message: > From: Michael Scheel <scheelmich...@googlemail.com> > Date: 10. Juni 2010 22:45:10 MESZ > To: Doug Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] advise on generating individual standard deviation > map > > Hi Doug, thanks for you reply. That is exactly what I want to do so many > thanks for explaining that. > However I have problems with the usage of mri_surf2surf > > michael$ mri_surf2surf --srcsubject bert --srcsurfval bert/surf/lh.thickness > --trgsubject fsaverage --trgsurfval bert/surf/lh.thickness_average --hemi lh > ERROR: could not determine type of bert/surf/lh.thickness_average > > Also when I run the example from the FS wiki site i get the following error > (see below). Any idea what I'm doing wrong here? > > Thanks, Michael > > michael$ mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness > --src_type curv --trgsubject ico --trgicoorder 7 --trgsurfval > bert-thickness-lh.img --trg_type analyze4d > srcsubject = bert > srcval = thickness > srctype = curv > trgsubject = ico > trgval = bert-thickness-lh.img > trgtype = analyze4d > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = (null) > label-trg = (null) > Reading source surface reg > /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.sphere.reg > Loading source data > Reading curvature file > /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.thickness > Reading icosahedron /Applications/MriSoftware/freesurfer/lib/bem/ic7.tri > Done > Mapping Source Volume onto Source Subject Surface > surf2surf_nnfr: building source hash (res=16). > Surf2Surf: Forward Loop (163842) > > surf2surf_nnfr: building target hash (res=16). > Surf2Surf: Reverse Loop (131122) > Reverse Loop had 21908 hits > Surf2Surf: Dividing by number of hits (163842) > INFO: nSrcLost = 0 > nTrg121 = 146869, nTrgMulti = 16973, MnTrgMultiHits = 2.29076 > nSrc121 = 89131, nSrcLost = 0, nSrcMulti = 41991, MnSrcMultiHits = 2.30095 > Saving target data > ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 > > > > > On 10.06.2010, at 12:05, Doug Greve wrote: > >> >> I don't have anything explicitly that will compute a map of z-scores, >> but you could do a two "group" analysis with your subject as the only >> one in one group and then do a group analysis. Alternatively, you can >> transform you individual to the fsaverage space (mri_surf2surf), then >> compute the z using fscalc.fsl. You'd have to compute the group mean >> and stddev using mri_concat (--mean and --std), then use fscalc.fsl, >> something like >> >> fscalc.fsl --surf fsaverage lh lh.thickness.fsaverage.mgh -sub >> groupmean.mgh -div groupstd.mgh zscore.mgh >> >> doug >> >> >> >> >> >> On Wed, 9 Jun 2010, Michael Scheel wrote: >> >>> Dear FS experts, >>> >>> could someone advise on how to create from an individual thickness file >>> (?h.thickness) a standard deviation or z-score map of the thickness with >>> respect to a control group. >>> >>> Thanks, Michael >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> -- >> 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 >> >> >> 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. >> >
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