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 Behalf
Of 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 probtrack
with 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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