All masks are where I expect them to be, but the exclusionmask contains
values of 0 and 0.9998... Running avwmaths <in> -bin <out> does not
solve this problem.
The path to the transformation matrix is fine, but applying the matrix
to mean_fsamples in standard space and comparing with the original
mean_fsamples shows some differences. The image histogram of the
difference image of these 2 mean_fsamples has a FWHH of about .05 and
95% of all voxels have a difference below 0.15. Is this a difference
that one would expect due to misregistration/interpolation?
Thanks,
Kerstin
----- Original Message -----
From: Matt <[log in to unmask]>
Date: Friday, July 6, 2007 10:55 am
Subject: Re: [FSL] problem with probtrack
> That syntax seems fine to me. You might verify that you can load
> all the
> masks (seed, targets, exclusion) you are calling in standard space in
> FSLView and make sure they are where you expect them to be (and
> have values
> of only 1 or 0). Also make sure your path to the transformation
> matrix is
> correct (and that the matrix itself is good). My guess would be
> that not
> everything is in the proper 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 8:43 PM
> To: [log in to unmask]
> Subject: Re: [FSL] problem with probtrack
>
> 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/me
> rged
> -m
>
/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/bedpost.bedpost/no
> dif_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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