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Hello,
I am trying to generate an inflated surface for a macaque brain, but mri_fill has stopped working for this subject. Below is my command line and output. I specify the corpus callosum and pons as well. Any suggestions?
mri_fill -CV 101 100 66 -PV 115 140 77 ./mri/wm/wm.nii.gz ./mri/filled/filled.mgz using voxel position (101, 100, 66) as corpus callosum seed point using voxel position (115, 140, 77) as pons seed point 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; Calculated talairach cc position (-8.26, -12.19, 56.63) Using the seed to calculate the cutting plane 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 seed (101, 100, 66), TAL = (-8.3, -12.2, 56.6) talairach voxel to 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; talairach cc position changed to (-8.26, -12.19, 56.63) Using voxel pons seed point, calculated talairach pons position (5.74, -1.19, 16.63) find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (115, 140, 77), TAL = (5.7, -1.2, 16.6) talairach voxel to 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; done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(9.74, -12.19, 56.63) SRC: (119.00, 100.00, 66.00) could not find rh seed point around (119, 100, 66)