# Tckgen: \[SYSTEM FATAL CODE: SIGSEGV (11)\] Segmentation fault: Invalid memory access (DYNAMIC SEEDING) **URL:** \ **Category:** Uncategorized\ **Tags:** troubleshooting, error\ **Created:** [May 7, 2024, 4:09pm UTC](https://community.mrtrix.org/t/tckgen-system-fatal-code-sigsegv-11-segmentation-fault-invalid-memory-access-dynamic-seeding/7593 "2024-05-07T16:09:35Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Hank\_Golding](https://community.mrtrix.org/user_avatar/community.mrtrix.org/hank_golding/32/4648_2.png) [@Hank\_Golding](https://community.mrtrix.org/u/Hank_Golding)\ **Post date:** [May 7, 2024, 4:09pm UTC](https://community.mrtrix.org/t/tckgen-system-fatal-code-sigsegv-11-segmentation-fault-invalid-memory-access-dynamic-seeding/7593/1 "2024-05-07T16:09:35Z")
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: ```auto 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 ---
**Author:** ![adsouza](https://community.mrtrix.org/user_avatar/community.mrtrix.org/adsouza/32/4571_2.png) [@adsouza](https://community.mrtrix.org/u/adsouza)\ **Post date:** [May 9, 2024, 11:57pm UTC](https://community.mrtrix.org/t/tckgen-system-fatal-code-sigsegv-11-segmentation-fault-invalid-memory-access-dynamic-seeding/7593/2 "2024-05-09T23:57:47Z")
Hi Hank, Does the 5TT image in this particular subject look sensible? Cheers, Arkiev ---
**Author:** ![Hank\_Golding](https://community.mrtrix.org/user_avatar/community.mrtrix.org/hank_golding/32/4648_2.png) [@Hank\_Golding](https://community.mrtrix.org/u/Hank_Golding)\ **Post date:** [May 16, 2024, 7:19pm UTC](https://community.mrtrix.org/t/tckgen-system-fatal-code-sigsegv-11-segmentation-fault-invalid-memory-access-dynamic-seeding/7593/3 "2024-05-16T19:19:41Z")
Apologies for the late response! I will double check but I believe good. Best, Hank