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
|