I am looking to visualize tracts from ProbtrackX using Chris Gorgolewski's BedpostX particle reader.
(I am looking to generate a connectivity matrix between atlas regions, and this is
is invaluable to me in visualizing the tracks. )
For this, I need to output particle files from ProbtrackX using the verbose==2 option, and then feed this to the
BedpostX particle reader to generate .trk files.
However, I have a major problem with my probtrackx output in that all my particle files are empty.
I have of course used the verbose==2 option and it does output normal fdt_paths.nii.gz ,
fdt_matrix1.dot, coords_for_fdt_matrix1 files.
But it keeps outputting empty particle files from particle0~particle99, and I have no idea why.
I have looked at the documentation for probtrackx2 and the internet, experimented with other options, but I cannot simply get it to work.
Any help would be greatly appreciated.
Regards, Tim Lyoo.
P.S
Any other workarounds that allow me to visualize the tracts from ProbtrackX (.trk for Trackvis is best, but a 3D representation would also be OK. ) would be a great help. Thanks!
Here is my probtrackx call.
/usr/local/fsl/bin/probtrackx2 -x /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/brodmann.nii.gz -V 2 -l --onewaycondition --omatrix1 -c 0.2 -S 2000 --steplength=0.5 -P 100 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/merged -m /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/nodif_brain_mask --dir=/home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/probtest3 >>probtest3/log
Here is the log file
Log directory is: /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/probtest3
basename /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/merged
maskfile /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/nodif_brain_mask
seeds /home/ylyoo3/URP_Finish/E/BEDPOSTX_raw/E_1.bedpostX/brodmann.nii.gz
output fdt_paths
verbose 2
nparticles 100
nsteps 2000
usef 0
rseed 12345
randfib 0
fibst 1
Running in seedmask mode
load seeds
done.
Load bedpostx samples
1_1
1_2
1_3
2_1
2_2
2_3
nfibres : 2
nsamples : 50
Done loading samples.
Initialise pathdist
....done
Volume seeds
volume 1
sl 0
sl 1
sl 2
sl 3
sl 4
sl 5
sl 6
sl 7
sl 8
sl 9
run
87 72 9
run
88 72 9
run
89 72 9
run
87 73 9
.....
72 65 74
run
73 65 74
run
74 65 74
run
75 65 74
sl 75
run
72 63 75
sl 76
sl 77
time spent tracking: 14894 seconds
save results
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