Hi Anna
This is very strange.. Could you make a tarball of all the files I need to replicate what you've done and upload it onto our server (instructions on the FSL wiki)
Cheers
Saad
On 23 Jan 2013, at 18:44, Anna Slagle wrote:
> Hello,
>
> On my most recent run of probtrackx2, I discovered that it seemed to ignore one of the exclusion masks (the last in a text file list of 9 exclusion masks). I rearranged the text file, moving the ignored mask to the top of the list, and re-ran probtrackx2. This time it seemed to obey all exclusion masks (even the newly last one in the list), so it apparently isn't an issue of too many exclusion masks. Has anybody else come across a similar issue? Should I be listing the exclusion masks in a particular order? Is there a maximum number of exclusion masks that can be implemented? Below is the command used.
>
>
> probtrackx2 -x roi1.nii -V 1 -l --pd --onewaycondition --wayorder -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=target_to_FA_warp.nii.gz --invxfm=FA_to_target_warp.nii.gz --avoid=exclusions.txt --stop=roi2.nii --forcedir --opd -s bedpostX/merged -m bedpostX/nodif_brain_mask --dir=right_AP --waypoints=waypoints.txt --waycond=AND
>
>
> Thank you for your help,
> Anna
>
>
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--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
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www.fmrib.ox.ac.uk/~saad
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