Kerstin,
If I understand correctly what you did, you should not apply transformation
matrices to the bedpost data. You should leave the bedpost outputs in
diffusion space and use the transformation matrix as the input in probtrack.
Regarding the masks, use avwmaths++ -in <maskfile> -div <maskfile> -out
<binarymask file> to get only ones and zeros.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Ms Kerstin Hoffmann
Sent: Thursday, July 05, 2007 9:49 PM
To: [log in to unmask]
Subject: Re: [FSL] problem with probtrack
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/std2d
iff.FA.mat
> --
>
rubbish=/data/home/kerstin/data/stroke_recovery/alldti/Ker_Hof.01/proc/exclu
sionmask.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/p
robtrack/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
> > >
> >
>
|