Hi!
Thanks for your help.
I checked my masks. They have all positive values, but my exclusionmask
contains 0 and 0.999... I created it using avwmaths -bin, and even
avwmaths exclusionmask -div exclusionmask exclusionmask does not give me
0 and 1.
The transformation matrix seems to be correct (as I can see it). I
applied it to my masks, and they are in the correct place.
Running in seed mask mode works, the pathway appears in the right place,
but it also travels into regions with low FA, too.
I also tried starting in single seed mode using the GUI without
exclusionmask, and probtrack didn't find a pathway at all. But when I
seed exactly the same voxel and use seed mask mode, everything works.
I don't know if there is any link, but another problem I have is that
when I draw a mask in fslview, I always have to apply avwswapdim -x y z,
as the left/right directions flip on saving.
number 992942. It contains the bedpost directory,
standard2diffusion-matrix, mean_fsamples and dyadic_vectors in standard
space, exclusionmask, seed mask (inclusionmask) and target mask
(mask.z90.2). I'd be very grateful if you could find a moment to have a
look at it and find out what is wrong.
Thanks again for your help.
Kersitn
----- Original Message -----
Date: Sunday, July 8, 2007 3:10 am
Subject: Re: [FSL] problem with probtrack
what happens if you run in seedmask mode with no target or rubbish
masks. Does the pathway appear in the right place.
My guess is the same as Matt's - there is something wrong with your
seed space to diffusion space transformation.
T
On 6 Jul 2007, at 10:25, Saad Jbabdi wrote:
Hi - Kerstin
For the single mode problem, make sure you provide the option --
seedref when using coordinates instead of a seed mask.
Concerning the seed_to_targets, I can't see any reason why it
doesn't work. Make sure all your target masks have positive
values,
your brain mask is binarised, etc.
If it still doesn't work, maybe you could upload your tar-gzipped
Cheers,
Saad.
On 6 Jul 2007, at 01:43, Ms Kerstin Hoffmann wrote:
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 -----
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
BehalfOf Ms Kerstin Hoffmann
Sent: Thursday, July 05, 2007 8:29 PM
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 -----
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-----
On
BehalfOf Ms Kerstin Hoffmann
Sent: Thursday, July 05, 2007 7:56 PM
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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Saad Jbabdi,
Postdoctoral Research Assistant,
Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222545 (fax 222717)
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