Hi Judit, we haven't run this a ton, so there certainly may still be problems in the algorithm. If you send us the dataset we'll take a look.
cheers, Bruce On Thu, 13 Aug 2009, Judit Haasz wrote: > Hi, > > I have run mri_cc -fornix. In some cases I encountered the following > problem. Although fornix.mgz was created, and it seems the program has > run properly, the file (same size as those who contain fornix) turns to > be empty. > Looking at the input volume, I could identify fornix. > Could you help finding a solution for my problem? > > Thank you for help! > Judit Haasz > > mri_cc -fornix -aseg aseg.auto_noCCseg.mgz -o fornix.mgz *SES > including fornix in segmentation > reading input aseg from aseg.auto_noCCseg.mgz > writing aseg with cc labels to fornix.mgz > reading aseg from > /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/aseg.auto_noCCseg.mgz > > reading norm from > /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/norm.mgz > 11261 voxels in left wm, 26612 in right wm, xrange [125, 132] > global minimum found at slice 128.0, rotations (0.25, -1.50) > final transformation (x=128.0, yr=0.250, zr=-1.500): > 1.000 0.026 0.004 -3.864; > -0.026 1.000 -0.000 3.409; > -0.004 0.000 1.000 0.560; > 0.000 0.000 0.000 1.000; > updating x range to be [126, 131] in xformed coordinates > best xformed slice 128 > cc center is found at 128 120 96 > eigenvectors: > -0.001 0.001 1.000; > -0.192 -0.981 0.001; > 0.981 -0.192 0.001; > error in mid anterior detected - correcting... > writing aseg with callosum to to > /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/fornix.mgz... > writing fornix to to > /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/fornix.mgz... > corpus callosum matter segmentation took 0.6 minutes > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
