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 scheelmichael@googlemail.com Date: 10. Juni 2010 22:45:10 MESZ To: Doug Greve greve@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
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