Thanks Moises,
I def. take a look at the tools you've provided.
The output files that I get in the .../probtrackx2/* . directory are:
coords_for_fdt_matrix1
probtrackx.log
tmpnetmask
1) Could you help me undestand the output of `coords_for_fdt_matrix1`the is the following:
$cat coords_for_fdt_matrix1
92 91 26 0 1
93 90 27 0 2
94 90 27 0 3
91 91 27 0 4
.
.
.
66 84 37 113 133192
67 84 37 113 133193
66 85 37 113 133194
Is it <x-coord> <y-coord> <z-coord> <???> <number_of_connected_paths>?
2) Should I assume the command didn't complete since fdt_path is not created?
Thanks in advance,
Rodrigo
<<<<<<<<
REPLIED FROM THESE PREVIOUS POSTS:
Hi Rodrigo,
I am not sure what are you trying to compute with probtrackx, and I am not sure how many seeds you are using for tracking,
but you are asking for:
--network: Matrix NROIS x NROIS
--matrix1: Matrix Nsees X Nseeds
--opd: path distribution map
I am not sure if you need all these things. Take a look at the documentation:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#PROBTRACKX_-_probabilistic_tracking_with_crossing_fibres
The first two options (network & matrix1), can be computationally very expensive. If you have an NVIDIA GPU you can use:
https://users.fmrib.ox.ac.uk/~moisesf/Probtrackx_GPU/
Moises.
On 6 February 2018 at 10:37, Rodrigo Perea <[log in to unmask]> wrote:
Hi probtrackx2 experts,
I run the following command:
/usr/pubsw/packages/fsl/5.0.9/bin/probtrackx2 --network -x .../seeds_mask_100_v1.txt -l --onewaycondition --omatrix1 -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s .../dmri.bedpostX/merged -m .../nodif_brain_mask --dir=.../probtrackx2
The output below (after ~15 hours) shows that there's been at least 33 volumes seeds processed.
So,
1) If seeds_mask_100_v1.txt has 100 volumes, it seems that it will take (15/33)*100 hours to finish the job?
2) If so, is there any way you could suggest to make this process run faster?
Thanks in advance,
Rodrigo
<OUTPUT>:
Log directory is: .../probtrackx2
Running in network mode
load seeds
Load bedpostx samples
1_1
1_2
1_3
2_1
2_2
2_3
nfibres : 2
nsamples : 50
Done loading samples.
Volume seeds
volume 0
volume 1
volume 2
volume 3
volume 4
volume 5
volume 6
volume 7
volume 8
volume 9
volume 10
volume 11
volume 12
volume 13
volume 14
volume 15
volume 16
volume 17
volume 18
volume 19
volume 20
volume 21
volume 22
volume 23
volume 24
volume 25
volume 26
volume 27
volume 28
volume 29
volume 30
volume 31
volume 32
volume 33
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