Hi Rob,
Thanks for your response!
I re-ran the code, this time without any mask, less confounding. But still there is huge difference between using two seeds/include and one seed/include. Here I posted the stdout, from two methods, as you can see, using two seeds and two include, resulted 48 streamlines, but using one seed and one include, resulted 1066 streamlines.
I uploaded the data I used to Drive(tractsDebug - Google Drive), just in case you want to replicate from your end. BTW, I’m using Ubuntu 20.04 and mrtrix (== mrinfo 3.0_RC3-1085-g4f819e7c ==)
two seeds and two include
Blockquote
mengxing@XPS:~/TESTDATA/local$ tckgen -algorithm iFoD2 -select 5000 -seed_image $sub/fs/ROIs/Left-LGN_dil-1.nii.gz -include $sub/fs/ROIs/Left-V1_dil-1.nii.gz -seed_image $sub/fs/ROIs/Left-V1_dil-1.nii.gz -include $sub/fs/ROIs/Left-LGN_dil-1.nii.gz -angle 45 -cutoff 0.05 -minlength 20 -maxlength 200 -stop $sub/mrtrix/dwi_wmCsd_autolmax_nomask.mif $sub/mrtrix/LOR2_6.tck -force -info -debug
tckgen: [WARNING] existing output files will be overwritten
tckgen: [DEBUG] No config file found at “/etc/mrtrix.conf”
tckgen: [DEBUG] No config file found at “/home/mengxing/.mrtrix.conf”
tckgen: [DEBUG] could not parse spherical ROI specification “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” - assuming mask image
tckgen: [INFO] opening image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] transforms_match: FOV difference in scanner coordinates: 3.9180703910543173e-06
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] Axes and transform of image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” altered to approximate RAS coordinate system
tckgen: [DEBUG] searching for suitable phase encoding data…
tckgen: [INFO] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” opened with dimensions 256x256x256, voxel spacing 1x1x1, datatype UInt8
tckgen: [DEBUG] loading image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [100%] uncompressing image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” initialised with strides = [ -1 65536 -256 ], start = 65535, using indirect IO
tckgen: [DEBUG] sanitising image information…
tckgen: [DEBUG] allocating scratch buffer for image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” initialised with strides = [ -1 1421 -29 ], start = 1420, using direct IO
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” unloaded
tckgen: [DEBUG] could not parse spherical ROI specification “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” - assuming mask image
tckgen: [INFO] opening image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] transforms_match: FOV difference in scanner coordinates: 3.9180703910543173e-06
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] Axes and transform of image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” altered to approximate RAS coordinate system
tckgen: [DEBUG] searching for suitable phase encoding data…
tckgen: [INFO] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” opened with dimensions 256x256x256, voxel spacing 1x1x1, datatype UInt8
tckgen: [DEBUG] loading image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [100%] uncompressing image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” initialised with strides = [ -1 65536 -256 ], start = 65535, using indirect IO
tckgen: [DEBUG] sanitising image information…
tckgen: [DEBUG] allocating scratch buffer for image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” initialised with strides = [ -1 156 -12 ], start = 155, using direct IO
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” unloaded
tckgen: [INFO] opening image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] transforms_match: FOV difference in scanner coordinates: 3.9180703910543173e-06
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] Axes and transform of image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” altered to approximate RAS coordinate system
tckgen: [DEBUG] searching for suitable phase encoding data…
tckgen: [INFO] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” opened with dimensions 256x256x256, voxel spacing 1x1x1, datatype UInt8
tckgen: [DEBUG] loading image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [100%] uncompressing image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” initialised with strides = [ -1 65536 -256 ], start = 65535, using indirect IO
tckgen: [DEBUG] sanitising image information…
tckgen: [DEBUG] allocating scratch buffer for image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” initialised with strides = [ -1 156 -12 ], start = 155, using direct IO
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” unloaded
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [INFO] opening image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] transforms_match: FOV difference in scanner coordinates: 3.9180703910543173e-06
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] Axes and transform of image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” altered to approximate RAS coordinate system
tckgen: [DEBUG] searching for suitable phase encoding data…
tckgen: [INFO] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” opened with dimensions 256x256x256, voxel spacing 1x1x1, datatype UInt8
tckgen: [DEBUG] loading image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [100%] uncompressing image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” initialised with strides = [ -1 65536 -256 ], start = 65535, using indirect IO
tckgen: [DEBUG] sanitising image information…
tckgen: [DEBUG] allocating scratch buffer for image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” initialised with strides = [ -1 1421 -29 ], start = 1420, using direct IO
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” unloaded
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [INFO] opening image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”…
tckgen: [DEBUG] reading key/value file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”…
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” opened with dimensions 104x104x72x45, voxel spacing 2.0192299999999999x2.0192299999999999x2x1, datatype Float32LE
tckgen: [DEBUG] memory-mapping file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”…
tckgen: [DEBUG] file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” mapped at 0x7effdba4f000, size 140175360 (read-only)
tckgen: [DEBUG] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” loaded
tckgen: [DEBUG] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” initialised with strides = [ 45 4680 486720 1 ], start = 0, using direct IO
tckgen: [INFO] step size = 1.00639975 mm
tckgen: [INFO] maximum angular change in fibre orientation per step = 45 deg
tckgen: [INFO] Minimum radius of curvature = 1.3149246mm
tckgen: [INFO] iFOD2 using 3 vertices per 1.00639975mm step
tckgen: [DEBUG] For tracking step size 1.00639975mm, max change in fibre orientation angle per step 45 deg (using RK4), minimum radius of curvature 1.31492mm, downsampling ratio 3: minimum length of 20mm requires at least 21 vertices pre-DS, is tested explicitly for 23 vertices or less post-DS; maximum length of 200mm will stop tracking after 600 vertices pre-DS, is tested explicitly for 199 or more vertices post-DS
tckgen: [DEBUG] creating empty file “sub18/mrtrix/LOR2_6.tck”
tckgen: [INFO] file “sub18/mrtrix/LOR2_6.tck” already exists - removing
tckgen: [INFO] rejection sampling will use 7 directions with a ratio of 2.15373945 (predicted number of samples per step = 12.9595909)
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “source”…
tckgen: [DEBUG] launching thread “sink”…
tckgen: [DEBUG] waiting for completion of threads “source”…
tckgen: [ 0%] 206451 seeds, 186301 streamlines, 1 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.254864097, max_val = 0.248964176)
tckgen: [ 0%] 505111 seeds, 455417 streamlines, 6 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.333255559, max_val = 0.30005464)
tckgen: [ 0%] 552601 seeds, 498258 streamlines, 7 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.308890939, max_val = 0.302813679)
tckgen: [ 0%] 673091 seeds, 606888 streamlines, 8 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.270945519, max_val = 0.270853788)
tckgen: [ 0%] 739021 seeds, 666269 streamlines, 9 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.262706727, max_val = 0.257611394)
tckgen: [ 0%] 830971 seeds, 749100 streamlines, 9 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.25940609, max_val = 0.255449086)
tckgen: [ 0%] 870341 seeds, 784524 streamlines, 9 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.258471906, max_val = 0.253768772)
tckgen: [ 0%] 927401 seeds, 835919 streamlines, 9 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.276347458, max_val = 0.271248609)
tckgen: [ 0%] 1113501 seeds, 1003852 streamlines, 12 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.256636232, max_val = 0.249747723)
tckgen: [ 0%] 1157301 seeds, 1043293 streamlines, 12 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.269458801, max_val = 0.262298465)
tckgen: [ 0%] 1716851 seeds, 1547681 streamlines, 23 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.297974795, max_val = 0.255817831)
tckgen: [ 0%] 1784351 seeds, 1608599 streamlines, 23 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.254709512, max_val = 0.252438724)
tckgen: [ 0%] 1837321 seeds, 1656291 streamlines, 23 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.296893001, max_val = 0.268821955)
tckgen: [ 0%] 1925661 seeds, 1735834 streamlines, 23 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.259857923, max_val = 0.258106768)
tckgen: [ 0%] 2264341 seeds, 2041196 streamlines, 27 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.321649313, max_val = 0.269435883)
tckgen: [ 0%] 2326491 seeds, 2097355 streamlines, 28 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.25367263, max_val = 0.25314182)
tckgen: [ 0%] 2472071 seeds, 2228619 streamlines, 30 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.245968476, max_val = 0.236088097)
tckgen: [ 0%] 2568901 seeds, 2315777 streamlines, 31 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.384820193, max_val = 0.345347673)
tckgen: [ 0%] 2661521 seeds, 2399278 streamlines, 31 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.354164332, max_val = 0.329433918)
tckgen: [ 0%] 2689541 seeds, 2424574 streamlines, 32 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.271914095, max_val = 0.258854926)
tckgen: [ 0%] 3088931 seeds, 2784826 streamlines, 34 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.295394003, max_val = 0.282667488)
tckgen: [ 0%] 3101441 seeds, 2796117 streamlines, 34 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.300877005, max_val = 0.29560855)
tckgen: [ 0%] 3769911 seeds, 3398829 streamlines, 39 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.236867711, max_val = 0.234286204)
tckgen: [ 0%] 4097771 seeds, 3694617 streamlines, 42 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.274844617, max_val = 0.261607111)
tckgen: [ 0%] 4392251 seeds, 3960088 streamlines, 43 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.262892336, max_val = 0.240138605)
tckgen: [ 0%] 4482191 seeds, 4041208 streamlines, 45 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.307391167, max_val = 0.267150313)
tckgen: [ 0%] 4495311 seeds, 4053016 streamlines, 45 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.252346843, max_val = 0.247654289)
tckgen: [ 0%] 4809341 seeds, 4335861 streamlines, 47 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.256309599, max_val = 0.244871408)
tckgen: [ 0%] 4993941 seeds, 4502074 streamlines, 48 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.276931375, max_val = 0.274493754)
tckgen: [ 0%] 4999871 seeds, 4507435 streamlines, 48 selected
tckgen: [DEBUG] no readers left on queue “source->sink”
tckgen: [DEBUG] no writers left on queue “source->sink”
tckgen: [DEBUG] threads “source” completed OK
tckgen: [DEBUG] waiting for completion of thread “sink”…
tckgen: [DEBUG] thread “sink” completed OK
tckgen: [100%] 5000000 seeds, 4507546 streamlines, 48 selected
tckgen: [INFO] mean number of samples per step = -nan
tckgen: [INFO] mean number of steps between rejection sampling truncations = -nan
tckgen: [INFO] maximum truncation error = 1.1937879323959351
tckgen: [INFO] Total number of track terminations: 9015260
tckgen: [INFO] Termination reason probabilities:
tckgen: [INFO] Calibrator sub-threshold: 100%
tckgen: [INFO] Exited image: 0%
tckgen: [INFO] Diffusion model sub-threshold: 0.0131%
tckgen: [INFO] Excessive curvature: 0%
tckgen: [INFO] Max length exceeded: 0.00205%
tckgen: [INFO] Traversed all include regions: 0.000821%
tckgen: [INFO] Track rejection counts:
tckgen: [INFO] Invalid seed point: 492460
tckgen: [INFO] No propagation from seed: 140135
tckgen: [INFO] Shorter than minimum length: 1227257
tckgen: [INFO] Missed inclusion region: 3140190
tckgen: [DEBUG] unmapping file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”
tckgen: [DEBUG] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” unloaded
tckgen: [DEBUG] deleting scratch buffer for image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” unloaded
tckgen: [DEBUG] deleting scratch buffer for image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” unloaded
tckgen: [DEBUG] deleting scratch buffer for image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” unloaded
tckgen: [DEBUG] deleting scratch buffer for image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” unloaded
one seed and one include
Blockquote
mengxing@XPS:~/TESTDATA/local$ tckgen -algorithm iFoD2 -select 5000 -seed_image $sub/fs/ROIs/Left-LGN_dil-1.nii.gz -include $sub/fs/ROIs/Left-V1_dil-1.nii.gz -angle 45 -cutoff 0.05 -minlength 20 -maxlength 200 -stop $sub/mrtrix/dwi_wmCsd_autolmax_nomask.mif $sub/mrtrix/LOR2_7.tck -force -debug
tckgen: [WARNING] existing output files will be overwritten
tckgen: [DEBUG] No config file found at “/etc/mrtrix.conf”
tckgen: [DEBUG] No config file found at “/home/mengxing/.mrtrix.conf”
tckgen: [DEBUG] could not parse spherical ROI specification “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” - assuming mask image
tckgen: [INFO] opening image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] transforms_match: FOV difference in scanner coordinates: 3.9180703910543173e-06
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] Axes and transform of image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” altered to approximate RAS coordinate system
tckgen: [DEBUG] searching for suitable phase encoding data…
tckgen: [INFO] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” opened with dimensions 256x256x256, voxel spacing 1x1x1, datatype UInt8
tckgen: [DEBUG] loading image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [100%] uncompressing image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” initialised with strides = [ -1 65536 -256 ], start = 65535, using indirect IO
tckgen: [DEBUG] sanitising image information…
tckgen: [DEBUG] allocating scratch buffer for image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” initialised with strides = [ -1 1421 -29 ], start = 1420, using direct IO
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” unloaded
tckgen: [INFO] opening image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] transforms_match: FOV difference in scanner coordinates: 3.9180703910543173e-06
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] Axes and transform of image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” altered to approximate RAS coordinate system
tckgen: [DEBUG] searching for suitable phase encoding data…
tckgen: [INFO] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” opened with dimensions 256x256x256, voxel spacing 1x1x1, datatype UInt8
tckgen: [DEBUG] loading image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [100%] uncompressing image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” initialised with strides = [ -1 65536 -256 ], start = 65535, using indirect IO
tckgen: [DEBUG] sanitising image information…
tckgen: [DEBUG] allocating scratch buffer for image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” loaded
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” initialised with strides = [ -1 156 -12 ], start = 155, using direct IO
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” unloaded
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “loop threads”…
tckgen: [DEBUG] waiting for completion of threads “loop threads”…
tckgen: [DEBUG] threads “loop threads” completed OK
tckgen: [INFO] opening image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”…
tckgen: [DEBUG] reading key/value file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”…
tckgen: [DEBUG] sanitising image information…
tckgen: [INFO] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” opened with dimensions 104x104x72x45, voxel spacing 2.0192299999999999x2.0192299999999999x2x1, datatype Float32LE
tckgen: [DEBUG] memory-mapping file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”…
tckgen: [DEBUG] file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” mapped at 0x7fa3e3a4f000, size 140175360 (read-only)
tckgen: [DEBUG] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” loaded
tckgen: [DEBUG] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” initialised with strides = [ 45 4680 486720 1 ], start = 0, using direct IO
tckgen: [INFO] step size = 1.00639975 mm
tckgen: [INFO] maximum angular change in fibre orientation per step = 45 deg
tckgen: [INFO] Minimum radius of curvature = 1.3149246mm
tckgen: [INFO] iFOD2 using 3 vertices per 1.00639975mm step
tckgen: [DEBUG] For tracking step size 1.00639975mm, max change in fibre orientation angle per step 45 deg (using RK4), minimum radius of curvature 1.31492mm, downsampling ratio 3: minimum length of 20mm requires at least 21 vertices pre-DS, is tested explicitly for 23 vertices or less post-DS; maximum length of 200mm will stop tracking after 600 vertices pre-DS, is tested explicitly for 199 or more vertices post-DS
tckgen: [DEBUG] creating empty file “sub18/mrtrix/LOR2_7.tck”
tckgen: [INFO] file “sub18/mrtrix/LOR2_7.tck” already exists - removing
tckgen: [INFO] rejection sampling will use 7 directions with a ratio of 2.15373945 (predicted number of samples per step = 12.9595909)
tckgen: [DEBUG] initialising threads…
tckgen: [DEBUG] launching 8 threads “source”…
tckgen: [DEBUG] launching thread “sink”…
tckgen: [DEBUG] waiting for completion of threads “source”…
tckgen: [ 1%] 396841 seeds, 396841 streamlines, 82 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.236962944, max_val = 0.233543977)
tckgen: [ 2%] 593511 seeds, 593511 streamlines, 115 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.312178135, max_val = 0.293956578)
tckgen: [ 3%] 1017881 seeds, 1017881 streamlines, 193 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.287869751, max_val = 0.233815059)
tckgen: [ 5%] 1481771 seeds, 1481771 streamlines, 291 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.258409858, max_val = 0.244873852)
tckgen: [ 16%] 3784061 seeds, 3784061 streamlines, 802 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.264128089, max_val = 0.255487531)
tckgen: [ 16%] 3803251 seeds, 3803251 streamlines, 804 selected
tckgen: [DEBUG] max_val exceeded!!! (val = 0.275974691, max_val = 0.262473255)
tckgen: [ 21%] 4999981 seeds, 4999981 streamlines, 1066 selected
tckgen: [DEBUG] no readers left on queue “source->sink”
tckgen: [DEBUG] no writers left on queue “source->sink”
tckgen: [DEBUG] threads “source” completed OK
tckgen: [DEBUG] waiting for completion of thread “sink”…
tckgen: [DEBUG] thread “sink” completed OK
tckgen: [WARNING] less than desired streamline number due to implicit maximum number of seeds; set -seeds 0 to override
tckgen: [100%] 5000000 seeds, 5000000 streamlines, 1066 selected
tckgen: [INFO] mean number of samples per step = -nan
tckgen: [INFO] mean number of steps between rejection sampling truncations = -nan
tckgen: [INFO] maximum truncation error = 1.2311856746673584
tckgen: [INFO] Total number of track terminations: 10000180
tckgen: [INFO] Termination reason probabilities:
tckgen: [INFO] Calibrator sub-threshold: 99.9%
tckgen: [INFO] Exited image: 0%
tckgen: [INFO] Diffusion model sub-threshold: 0.0116%
tckgen: [INFO] Excessive curvature: 0%
tckgen: [INFO] Max length exceeded: 0.0465%
tckgen: [INFO] Traversed all include regions: 0.016%
tckgen: [INFO] Track rejection counts:
tckgen: [INFO] Invalid seed point: 0
tckgen: [INFO] No propagation from seed: 13139
tckgen: [INFO] Shorter than minimum length: 85785
tckgen: [INFO] Missed inclusion region: 4900100
tckgen: [DEBUG] unmapping file “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif”
tckgen: [DEBUG] image “sub18/mrtrix/dwi_wmCsd_autolmax_nomask.mif” unloaded
tckgen: [DEBUG] deleting scratch buffer for image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-LGN_dil-1.nii.gz” unloaded
tckgen: [DEBUG] deleting scratch buffer for image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz”…
tckgen: [DEBUG] image “sub18/fs/ROIs/Left-V1_dil-1.nii.gz” unloaded