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. > > 3) 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: > > 4) 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 > > > _______________________________________________ > 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 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.
