Seed mask and target mask are in standard space, i am using the option
--xfm=<standard2diffsion-matrix>.
probtrack.log contains this output:
/usr/share/fsl/bin/probtrack --mode=seeds_to_targets -x
/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/proc/inclusionmask.nii.gz
--forcedir -s
/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/bedpost.bedpost/merged
-m
/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/bedpost.bedpost/nodif_brain_mask
--xfm=/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/proc/mat/std2diff.FA.mat
--rubbish=/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/proc/exclusionmask.nii.gz
-l -c 0.2 -S 2000 --steplength=0.5 -P 300
--targetmasks=/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/proc/probtrack/seeds2targets/targets.txt
--dir=/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/proc/probtrack/seeds2targets
Kerstin
----- Original Message -----
From: Matt <[log in to unmask]>
Date: Friday, July 6, 2007 10:31 am
Subject: Re: [FSL] problem with probtrack
> Can you post your probtrack.log output? Also, are you doing
> everything in
> native space?
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> BehalfOf Ms Kerstin Hoffmann
> Sent: Thursday, July 05, 2007 8:29 PM
> To: [log in to unmask]
> Subject: Re: [FSL] problem with probtrack
>
> Yes, the diffusion directions are correctly orientated. Using
> probtrackwith seed mask option on my data gives results that are
> close to my
> expectations as well. The problem only occurs when using single seed
> voxel and connectivity based seed classification.
> Thanks for you help.
> Kerstin
>
>
> ----- Original Message -----
> From: Matt <[log in to unmask]>
> Date: Friday, July 6, 2007 10:06 am
> Subject: Re: [FSL] problem with probtrack
> > Did you verify that your diffusion directions are correctly
> > oriented with
> > respect to what you would expect anatomically (by loading the FA
> > and V1 with
> > lines)?
> >
> > Peace,
> >
> > Matt.
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On
> > BehalfOf Ms Kerstin Hoffmann
> > Sent: Thursday, July 05, 2007 7:56 PM
> > To: [log in to unmask]
> > Subject: [FSL] problem with probtrack
> >
> > Hi!
> > I just ran into a problem using the connectivity based
> > seed-classification option in probtrack. Using all brain voxels
> (FA >
> > 0.1) as seed mask and an axial cut of the internal capsule as target
> > (number of samples 300), I got only about 15 voxels with
> intensity >0.
> > Using a seed mask inside the internal capsule and a target mask
> > right on
> > top of it returned equally poor results.
> > Also, when I use the single seed voxel option, the output file
> > containsno voxels with intensity >0, but using the same voxel in
> > seed mask
> > option, I get results that look fine.
> > I also ran FEEDS, and no problems were reported.
> > Any advice would be greatly appreciated.
> > Thanks
> > Kerstin
> >
>
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