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FSL  July 2007

FSL July 2007

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Subject:

Re: problem with probtrack

From:

Ms Kerstin Hoffmann <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 9 Jul 2007 08:47:53 +1000

Content-Type:

text/plain

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text/plain (185 lines)

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.
I uploaded my data on www.fmrib.ox.ac.uk/cgi-bin/upload.cgi, reference
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 -----
From: Tim Behrens <[log in to unmask]>
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 
> 
> > data at www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and we'll have a look.
> >
> > 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 -----
> >> 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
> >>>>
> >>>
> >
> > ------------------------------------------------------------------
> ---- 
> > -----
> > Saad Jbabdi,
> > Postdoctoral Research Assistant,
> > Oxford University FMRIB Centre
> >
> > FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> > +44 (0) 1865 222545  (fax 222717)
> > [log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
> > ------------------------------------------------------------------
> ---- 
> > -----
> >
> >
> >
> >
> 
> 

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