Dear MRtrix Experts
I am trying to run whole-brain ACT with dynamic seeding. For about 2/3 of my adult cohort (b=1000) it runs through without any problems. But for the remaining subjects, the tckgen command can’t finish after “waiting for completion of threads “source”…”. I tried to run it with number of threads = 0, however after 15 hours still nothing happend. Has anyone an idea what I could try next to make it work for my remaining subjects? Your help is much appreciated!
You can find more info below.
Thank you!
Anna
I am using the following tckgen version:
== tckgen 3.0_RC3-212-gf2ed89d8 ==
64 bit release version, built Aug 29 2019, using Eigen 3.2.92
My command was the following:
/home/fsl/mrtrix3/bin/tckgen -force -debug -info -act 5tt_regtodwi.mif -backtrack -seed_dynamic wmfod_norm.mif -select 10000000 wmfod_norm.mif tracks_10mio.tck
You can find the last part of my debugging output here:
....
.....
tckgen: [DEBUG] failed to find SH peak!
tckgen: [DEBUG] failed to find SH peak!
tckgen: [DEBUG] failed to find SH peak!
tckgen: [DEBUG] no writers left on queue "pipe->sink"
tckgen: [DEBUG] no readers left on queue "source->pipe"
tckgen: [DEBUG] threads "pipe" completed OK
tckgen: [DEBUG] waiting for completion of thread "sink"...
tckgen: [DEBUG] no readers left on queue "pipe->sink"
tckgen: [DEBUG] thread "sink" completed OK
tckgen: [100%] segmenting FODs
tckgen: [INFO] opening image "wmfod_norm.mif"...
tckgen: [DEBUG] reading key/value file "wmfod_norm.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "wmfod_norm.mif" opened with dimensions 112x112x60x45, voxel spacing 2x2x2x1, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "wmfod_norm.mif"...
tckgen: [DEBUG] file "wmfod_norm.mif" mapped at 0x7f9317ecb000, size 135475200 (read-only)
tckgen: [DEBUG] image "wmfod_norm.mif" loaded
tckgen: [DEBUG] image "wmfod_norm.mif" initialised with strides = [ 45 -5040 564480 1 ], start = 559440, using direct IO
tckgen: [INFO] opening image "5tt_regtodwi.mif"...
tckgen: [DEBUG] reading key/value file "5tt_regtodwi.mif"...
tckgen: [DEBUG] sanitising image information...
tckgen: [INFO] image "5tt_regtodwi.mif" opened with dimensions 112x112x60x5, voxel spacing 2x2x2x1, datatype Float32LE
tckgen: [DEBUG] memory-mapping file "5tt_regtodwi.mif"...
tckgen: [DEBUG] file "5tt_regtodwi.mif" mapped at 0x7f9453525000, size 15052800 (read-only)
tckgen: [DEBUG] image "5tt_regtodwi.mif" loaded
tckgen: [DEBUG] image "5tt_regtodwi.mif" initialised with strides = [ -1 112 12544 752640 ], start = 111, using direct IO
tckgen: [INFO] step size = 1 mm
tckgen: [INFO] maximum deviation angle = 45 deg
tckgen: [INFO] minimum radius of curvature = 1.9999999443449312 mm
tckgen: [INFO] iFOD2 internal step size = 0.333333343 mm
tckgen: [DEBUG] creating empty file "tracks_10mio.tck"
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 64 threads "source"...
tckgen: [DEBUG] launching thread "pipe1"...
tckgen: [DEBUG] launching 64 threads "pipe2"...
tckgen: [DEBUG] launching thread "sink"...
tckgen: [DEBUG] waiting for completion of threads "source"...