Hello FSL List,
I am currently trying to run probtrackx from freesurfer cortical surfaces using FSL (5.0.6), however my fdt_path.nii.gz output file does not seem to show any sort of streamline output.
I have registered FreeSurfer conformed structural space to diffusion space and created a label file using tksurfer (as described on http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fdt/fdt_surface.html), however the following step, running probtrackx, seems to be the problem. This is what I currently have typed in my command line when I am trying to run probtrackx, and the following output:
probtrackx –samples=/media/BEDPOSTX.bedpostX/merged --mask=/Diffusion/nodif_brain_mask.nii.gz -x /media/label/rh.fctest.label --mesh=/surf/rh.white.asc --xfm=/media/freesurfer2fa.mat --seedref=/nifti/brain.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -V 2 --mode=seedmask
Log directory is: logdir
basename /media/BEDPOSTX.bedpostX/merged
maskfile /Diffusion/nodif_brain_mask.nii.gz
seeds /media/label/rh.fctest.label
output fdt_paths
verbose 2
nparticles 50
nsteps 2000
usef 0
rseed 12345
randfib 0
fibst 1
loading mesh files
mesh files loaded
1_1
1_2
1_3
2_1
2_2
2_3
7
I am not sure what exactly is wrong here and why I am not getting the proper output file. I have followed the instructions on the page step by step, and have also checked over my command line to make sure all the directories are correct.
Any help would be appreciated!
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