Hi India!
This is a bit confusing. Can you clarify please:
1. is fdt_paths there but empty, or is it not there at all?
2. when you run probtrackx with NO targets, you shouldn't be getting
the files fdt_seed_classification.txt ad targets.txt... Are you sure
you are looking at the right files in the right directories? (you can
check the time they were created, this will tell you if they
correspond to that probtrackx run).
Note that if fdt_paths is there but empty, that means there was no
accepted tract, either because no tract gets to the waypoints masks,
or because they are all outside your brain. This last bit can happen
if your seed/targets are not in diffusion space, in which case you
need to input the FLIRT transform from seed space to diffusion space.
Cheers,
Saad.
On 22 Nov 2008, at 23:16, India Bohanna wrote:
> Hi. Thanks for your help with this.
>
> When I run probtrackx with no targets or waypoints, I get the files
> core, fdt.log,
> fdt_seed_classification.txt, probtrackx.log, targets.txt and
> waypoints.txt. I do not get an
> fdt_paths output file.
>
> The command I'm using:
>
> probtrackx --mode=seedmask -x
> P206_dti_FA_orig_ROI_FA_UHDRS_mask_cc.nii.gz -l -c 0.2
> -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s
> Bedpost.bedpostX/merged -m
> Bedpost.bedpostX/nodif_brain_mask --dir=P206/track/UHDRS/Left --
> waypoints=/P206/track/UHDRS/Left/waypoints.txt --
> targetmasks=P206/track/UHDRS/Left/targets.txt --os2t
>
> Thanks
> India
>
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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