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>( 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
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