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