Dear Saad,

 

I’ve checked the two things but no luck. So I uploaded the file. The ID # is 324683.

Thank you very much.

 

Regards,

-Hu

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Saad Jbabdi
Sent: Friday, February 09, 2007 9:37 AM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack - no connectivity generated

 

Hi,

 

I can't see what's happening here.

Could you try :

* check whether the voxel 88,52,11 is inside the brain mask

> avwstats results88_52_11 -r -R    (to check whether the output values are all zeros).

 

If these two don't help, then could you upload your tar-gzipped bedpost directory in www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and send us the ID, we'll have a look.

 

Thanks,

Saad

 

 

 

On 9 Feb 2007, at 14:16, Cheng, Hu wrote:



Hi, Matt,

 

I don’t see probtrack.log, but there is a file called fdt.log. The content is as following:

 

set tool probtrack

set probtrack(bedpost_dir) /usr/local/data/DTI/subj3.bedpost

set probtrack(xfm)

set probtrack(mode) simple

set probtrack(exclude_yn) 0

set probtrack(usereference_yn) 0

set probtrack(verbose_yn) 0

set probtrack(loopcheck_yn) 1

set probtrack(modeuler_yn) 0

set probtrack(curvature) 0.2

set probtrack(nsteps) 2000

set probtrack(steplength) 0.5

set probtrack(nparticles) 5000

set probtrack(x) 88

set probtrack(y) 52

set probtrack(z) 11

set probtrack(units) vox

set probtrack(output) results

 

Thanks.

 

Regards,

-Hu

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matt
Sent: Thursday, February 08, 2007 2:18 PM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack - no connectivity generated

 

Hu,

 

Can you post the contents of probtrack.log?  It will be in the folder where you saved your results.

 

Peace,

 

Matt.

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Cheng, Hu
Sent: Thursday, February 08, 2007 2:03 PM
To: [log in to unmask]
Subject: [FSL] ProbTrack - no connectivity generated

 

Dear FSL user,

 

We tried to get a fiber out of the DTI images. The DTIFit and BEDPOST ran well and the results looked reasonable. There was no error message after we performed the ProbTrack, however, the resulted image was 0 everywhere. We couldn’t see any non-zero values even at the seed voxel. We changed the seed location, but this remained the same. Does anyone know what the problem is? Thanks.

 

Hu Cheng, Ph.D.
MRI Physicist, Imaging Research Facility
Department of Psychological and Brain Sciences
Indiana University
Bloomington, IN 47405
Tel. 812-856-2518
Fax. 812-855-4691

 



 

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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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