What's your command line? Are you using voxel coords?
On Jun 7, 2012, at 9:52 PM, Shay Ohayon <shay.oha...@gmail.com> wrote: > Hi, > > I am having problem getting mri_fill to run on one of my volumes (it did work > with another monkey, so I assume I am running things right). > I am using v5.0 (but it also happens on 5.1). > The input is a monkey wm file with specified coordinates for the corpus > callosum. > The error I get is: "could not find corpus callosum" (see full log below). > The input volume is available for download here > (http://tsaolab.caltech.edu/sites/default/files/wm.mgz) > > Any takers? I tried various different coordinates and all of them fail. > A hint may be this statement: "find_cutting_plane:seed point not in > structure! Searching neighborhood..." > which I don't fully understand as the point given is inside a connected > component... > > Many thanks, > > Shay > Tsao Lab > Caltech > > > > > --------------------------- > > reading input volume...done. > searching for cutting planes...INFO: volume does not have linear_transform > set nor lta is given by option.-xform. > INFO: use identity matrix as the talairach transform. > INFO: use src volume parameters for the talairach volume. > voxel to talairach voxel transform > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > find_cutting_plane:seed point not in structure! Searching neighborhood... > Looking for area (min, max) = (350, 1400) > area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) > need search nearby > using +/- offset search region where offset is 3..... > using +/- offset search region where offset is 6..... > using +/- offset search region where offset is 9..... > using +/- offset search region where offset is 12..... > using +/- offset search region where offset is 15..... > using +/- offset search region where offset is 18..... > using +/- offset search region where offset is 21..... > using +/- offset search region where offset is 24..... > using +/- offset search region where offset is 27..... > using +/- offset search region where offset is 30..... > using +/- offset search region where offset is 33..... > using +/- offset search region where offset is 36..... > using +/- offset search region where offset is 39..... > using +/- offset search region where offset is 42..... > using +/- offset search region where offset is 45..... > using +/- offset search region where offset is 48..... > /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill: > could not find corpus callosum > /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill > /space/data/shayo/cooked/test2/mri/wm.nii > /space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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