Hello all,
I am running MRTrix3 3.0.4, producing connectomes with dynamic seeding using tckgen with the IFOD2 option. I have run this command on 10 brains - 9 work perfectly, one repeatedly fails:
tckgen: [DEBUG] No config file found at "/etc/mrtrix.conf"
tckgen: [DEBUG] No config file found at "/home/sg526/.mrtrix.conf"
tckgen: [INFO] opening image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif"...
tckgen: [DEBUG] reading key/value file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" opened with dimensions 140x140x140x45, voxel spacing 1.7x1.7x1.7x1, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif"...
tckgen: [DEBUG] file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" mapped at 0x7f5ce8df2000, size 493920000 (read-only)
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" loaded
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" initialised with strides = [ -45 6300 882000 1 ], start = 6255, using direct IO
tckgen: [DEBUG] sanitising image information...
tckgen: [DEBUG] allocating scratch buffer for image "fixel map voxels"...
tckgen: [DEBUG] image "fixel map voxels" loaded
tckgen: [DEBUG] image "fixel map voxels" initialised with strides = [ -1 140 19600 ], start = 139, using direct IO
tckgen: [DEBUG] sanitising image information...
tckgen: [DEBUG] allocating scratch buffer for image "SIFT model processing mask"...
tckgen: [DEBUG] image "SIFT model processing mask" loaded
tckgen: [DEBUG] image "SIFT model processing mask" initialised with strides = [ -1 140 19600 ], start = 139, using direct IO
tckgen: [INFO] opening image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] reading key/value file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" opened with dimensions 140x140x140x5, voxel spacing 1.7x1.7x1.7xnan, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" mapped at 0x7f5ce3a33000, size 54880000 (read-only)
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" loaded
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" initialised with strides = [ 5 700 98000 1 ], start = 0, using direct IO
tckgen: [DEBUG] sanitising image information...
tckgen: [DEBUG] allocating scratch buffer for image "5TT scratch buffer"...
tckgen: [DEBUG] image "5TT scratch buffer" loaded
tckgen: [DEBUG] image "5TT scratch buffer" initialised with strides = [ -5 700 98000 1 ], start = 695, using direct IO
tckgen: [INFO] 5TT image dimensions match fixel image - importing directly
tckgen: [DEBUG] unmapping file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" unloaded
tckgen: [INFO] opening image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] reading key/value file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" opened with dimensions 140x140x140x5, voxel spacing 1.7x1.7x1.7xnan, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" mapped at 0x7f5ce3a33000, size 54880000 (read-only)
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" loaded
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" initialised with strides = [ 5 700 98000 1 ], start = 0, using direct IO
tckgen: [100%] segmenting FODs
tckgen: [INFO] opening image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif"...
tckgen: [DEBUG] reading key/value file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" opened with dimensions 140x140x140x45, voxel spacing 1.7x1.7x1.7x1, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif"...
tckgen: [DEBUG] file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" mapped at 0x7f5cc2ed0000, size 493920000 (read-only)
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" loaded
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/msmt-csd_wmfod.mif" initialised with strides = [ -45 6300 882000 1 ], start = 6255, using direct IO
tckgen: [INFO] opening image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] reading key/value file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" opened with dimensions 140x140x140x5, voxel spacing 1.7x1.7x1.7xnan, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif"...
tckgen: [DEBUG] file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" mapped at 0x7f5cbfa79000, size 54880000 (read-only)
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" loaded
tckgen: [DEBUG] image "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/temp/5tt_coreg.mif" initialised with strides = [ 5 700 98000 1 ], start = 0, using direct IO
tckgen: [INFO] step size = 0.850000024 mm
tckgen: [INFO] maximum angular change in fibre orientation per step = 35 deg
tckgen: [INFO] Minimum radius of curvature = 1.41334164mm
tckgen: [INFO] iFOD2 generating 3 vertices per 0.850000024 mm step
tckgen: [DEBUG] For tracking step size 0.850000024mm, max change in fibre orientation angle per step 35 deg (using RK4), minimum radius of curvature 1.41334mm, downsampling ratio 3: minimum length of 10mm requires at least 13 vertices pre-DS, is tested explicitly for 15 vertices or less post-DS; maximum length of 170mm will stop tracking after 603 vertices pre-DS, is tested explicitly for 200 or more vertices post-DS
tckgen: [DEBUG] creating empty file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/sub-ses-baselineYear1Arm1_msmt-csd_ifod2_dynamic_200K.tck"
tckgen: [INFO] file "/n/scratch/users/c/cs126/DTI_DATA/sub/ses-baselineYear1Arm1/dwi/sub-ses-baselineYear1Arm1_msmt-csd_ifod2_dynamic_200K.tck" already exists - removing
tckgen: [INFO] rejection sampling will use 7 directions with a ratio of 1.40719807 (predicted number of samples per step = 9.7517786)
tckgen: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access
I’ve created connectomes with ifod2 gmwmi seeding with this brain and these .mif files. Any help would be greatly greatly appreciated.
Thanks!!
Hank