Hi Cedric, try it with --noreshape. If you're using mgh format, then reshaping is not necessary. doug On 01/22/2013 09:16 AM, Koolschijn, Cédric wrote:
Hi Doug and other FS-experts,
I succesfully applied the registration step of the Cortical Thickness of a Volume-defined ROI wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness However, I'm having troubles at the end.
- Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI
surface overlay. This works perfectly: (fsaverage dir)
mri_vol2surf --mov ../../Parietal_Sup_L152.nii --reg ../../test.register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fs.average.parietal.mgh --reshape
Then viewing: tksurfer fsaverage lh inflated -overlay lh.fsaverage.parietal.mgh -fthresh 0.5 Is also perfect.
The problem arises in step 4/5. First:
- Map your subject thickness data to the fsaverage subject. Do this for
all your subjects. mri_surf2surf --s BT1P0392_9_1 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
srcsubject = BT1P0392_9_1 srcval = lh.thickness srctype = trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//BT1P0392_9_1/surf/lh .sphere.reg Loading source data Reading target surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//fsaverage/surf/lh.sp here.reg 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 (144750) Reverse Loop had 31554 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141619, nTrgMulti = 22223, MnTrgMultiHits = 2.41988 nSrc121 = 107010, nSrcLost = 0, nSrcMulti = 37740, MnSrcMultiHits = 2.34197 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh
Here all is well. But then: 5) Run mri_segstats, using the subject-ROI surface, to get the thickness data for your ROI.
mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt
$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt sysname Linux hostname corleone01univ.nl machine x86_64 user cedric Loading /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7
If I then follow the suggestion to use the --reshape-factor 7 and re-run steps 4 and 5, I keep on getting the same error message " ERROR: dimension mismatch between input volume and seg".
Do you have any ideas what is going (wr)on(g)?
Many thanks, Cédric
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