Hi Francis,
I cannot reproduce this from my side. Can you send us your seed masks?
Saad.
On 22 Mar 2010, at 01:38, Francis Wong wrote:
> Hi Matt,
>
> Sure.
>
> I used the GUI and here are the logs:
>
> <probtrackx.log>
> /usr/local/fsl/bin/probtrackx --network --mode=seedmask -x
> /home/FSL/fsl_course_data/fdt/Tha-Pre/masks.txt -l -c 0.2 -S 2000 --steplength=0.5 -P
> 5000 --xfm=/home
> /FSL/fsl_course_data/fdt/subj1_2fibres.bedpostX/xfms/standard2diff.mat --forcedir --opd
> -s /home /FSL/fsl_course_data/fdt/subj1_2fibres.bedpostX/merged -m /home
> /FSL/fsl_course_data/fdt/subj1_2fibres.bedpostX/nodif_brain_mask --
> dir=/home/FSL/fsl_course_data/fdt/Tha-Pre
> ---------------------------------------------
>
>
> <masks.txt>
> /home/Francis/home/MRITemplates/HarvardOxford-cort/Postcentral_Gyrus.nii.gz
> /home/Francis/home/MRITemplates/HarvardOxford-subcort/Left_Thalamus.nii.gz
>
>
>
> <fdt.log>
> set tool probtrackx
> set probtrack(usereference_yn) 1
> set probtrack(xfm)
> /home/FSL/fsl_course_data/fdt/subj1_2fibres.bedpostX/xfms/standard2diff.mat
> set probtrack(bedpost_dir) /home/FSL/fsl_course_data/fdt/subj1_2fibres.bedpostX
> set probtrack(xfm)
> /home/FSL/fsl_course_data/fdt/subj1_2fibres.bedpostX/xfms/standard2diff.mat
> set probtrack(mode) network
> set probtrack(exclude_yn) 0
> set probtrack(usereference_yn) 1
> 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
> .fdt.data.seed.targets insert end /home/Francis/home/MRITemplates/HarvardOxford-
> cort/Postcentral_Gyrus.nii.gz /home/Francis/home/MRITemplates/HarvardOxford-
> subcort/Left_Thalamus.nii.gz
> set probtrack(reference)
> set probtrack(output) /home/FSL/fsl_course_data/fdt/Tha-Pre
>
>
>
>
> Thanks a lot
> Francis
>
>
> On Sun, 21 Mar 2010 20:17:54 -0500, Matt Glasser <[log in to unmask]> wrote:
>
>> Can you provide the commandline you used for probtrackx or the contents of
>> probtrackx.log?
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>> Of Francis Wong
>> Sent: Sunday, March 21, 2010 7:22 PM
>> To: [log in to unmask]
>> Subject: [FSL] FDT Multiple masks - all zeros
>>
>> Hi,
>>
>> I am having troubles with PROBTRACKX with multiple masks as seeds. Simply
>> put, I got
>> images with all zeros after running PROBTRACKX.
>>
>> For example, with the sample DTI data in the FSL course materials, I tried
>> using the
>> thalamus and the precentral gyrus as the seeds in Multiple masks mode
>> without any
>> targets, I can't find a single non-zero voxel in the output of FDT.
>>
>> I am quite confident with the data preprocessing steps because I did get
>> sensible tracks, for
>> example, using pSTG as the seed mask, I am able to get the tracks projecting
>> to the IFG.
>> But when I no tracks were found with pSTG and IFG as the seed masks.
>>
>> Is there any sample data showing what an output would look like with
>> multiple masks
>> mode?
>>
>> Any input from you guys would be much appreciated.
>>
>> Thanks,
>> Francis
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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