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:
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
Tel. 812-856-2518
Fax. 812-855-4691
---------------------------------------------------------------------------
Saad Jbabdi,
Postdoctoral Research
Assistant,
FMRIB, JR Hospital,
Headington,
+44 (0) 1865
222545 (fax 222717)
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