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Thanks so much! I had missed the patch. I'll upgrade. -Dianne On Fri, May 15, 2009 at 2:16 AM, Saad Jbabdi <[log in to unmask]> wrote: > Hi Dianne, > > If you are using FSL4.1.3 and above, then a streamline should stop whenever > entering a termination mask. This means that if you start from a termination > mask, you shouldn't be able to track at all! > > Which makes me think that perhaps you are using FSL4.1.2 or below? In this > case, the termination mask will not be "active" until you leave it first > (which allows you to track from a termination mask). > > In my opinion, you should either use the csf as a termination mask (with a > more recent version of FSL), or use the tissue mask as a brain mask (ie the > -m option). > > > Cheers, > Saad. > > > On 14 May 2009, at 22:01, Dianne Patterson wrote: > > Dear Group, > I am running probtrack on patients with strokes and primary progressive > aphasia. > I recently discovered that probtrack seemed perfectly happy to track > through csf-filled lesions. > This seemed inappropriate, so I set about creating a termination mask to > stop tracking if it exited the tissue and entered csf. > > My understanding is that as fsl currently works, the termination mask is > the tissue mask and not the csf mask itself. > My tissue termination mask definitely improves things, but apparently > probtrack can still enter forbidden territory > (csf that is not included in my tissue mask). > I'm trying to figure out if I've done something wrong or if it is working > as it should (just not as I expected). > > Here's an example of my command for the inferior occipital fasciculus: > > probtrackx --network --mode=seedmask -x iof_l_csf/masks.txt -l -c 0.2 -S > 2000 --steplength=0.5 -P 5000 --avoid=ProbROIs/iof_l_exclusion_diff.nii.gz > --stop=ProbROIs/nodif_gw.nii.gz --forcedir -f --opd -s Bed.bedpostX/merged > -m Bed.bedpostX/nodif_brain_mask --dir=iof_l_csf > > The masks specified in iof_l_csf/masks.txt are trimmed so that they don't > overlap the csf. > The exclusion mask is just the opposite hemisphere. > The termination mask: --stop=ProbROIs/nodif_gw.nii.gz is everything that is > tissue (non-csf). > > The results show that on occasion fdt_paths still includes voxels that are > beyond my termination mask. > Is this expected behavior? > Would it be reasonable to just use fslmaths to multiply fdt_paths by the > tissue mask and enforce the restriction...or am I missing something more > fundamental? > > Thanks for your time, > > Dianne > --------------------------------------------- > -- > Dianne Patterson, Ph.D. > [log in to unmask] > University of Arizona > SLHS 328 > 621-5105 > > > Saad Jbabdi > Oxford University FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > +44 (0) 1865 222545 (fax 717) > www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad> > > > > > > > -- Dianne Patterson, Ph.D. [log in to unmask] University of Arizona SLHS 328 621-5105