Dear FreeSurfer experts,
I'm attempting to make cortical surfaces for a macaque brain, and am having trouble getting mri_fill to work. The command has worked without any errors for a different macaque dataset in the past, and I can't seem to figure out why it isn't working this time.
I am using v. 5.3 for Mac Snow Leopard, and I used the command (I have confirmed on tkmedit that the CC and pons seed coordinates are correct): *mri_fill -CV 125 119 147 -PV 125 103 65 wm.mgz fill.mgz*
The log from running the command is as follows: -------------------------------------------------------------------------------------------------------- using voxel position (125, 119, 147) as corpus callosum seed point using voxel position (125, 103, 65) 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 (125.00, 119.00, 147.00) 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 (125, 119, 147), TAL = (125.0, 119.0, 147.0) 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 (125.00, 119.00, 147.00) Using voxel pons seed point, calculated talairach pons position (125.00, 103.00, 65.00) 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 (125, 103, 65), TAL = (125.0, 103.0, 65.0) 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:(143.00, 119.00, 147.00) SRC: (143.00, 119.00, 147.00) could not find rh seed point around (143, 119, 147) ------------------------------------------------------------------------------------------------------------
Any help with this would be greatly appreciated.
Best, Soyoung