Dear experts,

I am looking at a puzzling issue related to the use of both --waypoints and --stop options in probtrackx and probtrackx2.

The following show examples of how I call these two commands:

probtrackx --mode=seedmask -x /users/cais/STUT/analysis/aparc12_tracts_2/S01/aparc12_lh_vMC.diff.nii.gz -s /users/cais/STUT/analysis/dti2/tracula/S01/dmri.bedpostX/merged -m /users/cais/STUT/analysis/dti2/tracula/S01/dmri/nodif_brain_mask.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd --pd --dir=/users/cais/STUT/analysis/aparc12_pt2_roi2roi/S01/lh_vMC-lh_vSC --stop=/users/cais/STUT/analysis/aparc12_tracts_2/S01/aparc12_lh_vSC.diff.nii.gz --waypoints=/users/cais/STUT/analysis/aparc12_tracts_2/S01/aparc12_lh_vSC.diff.txt --avoid=/users/cais/STUT/FSDATA/S01/mri/ccMask_diff.nii.gz

probtrackx2 --mode=seedmask -x /users/cais/STUT/analysis/aparc12_tracts_2/S01/aparc12_lh_vMC.diff.nii.gz -s /users/cais/STUT/analysis/dti2/tracula/S01/dmri.bedpostX/merged -m /users/cais/STUT/analysis/dti2/tracula/S01/dmri/nodif_brain_mask.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd --pd --dir=/users/cais/STUT/analysis/aparc12_pt2_roi2roi/S01/lh_vMC-lh_vSC --stop=/users/cais/STUT/analysis/aparc12_tracts_2/S01/aparc12_lh_vSC.diff.nii.gz --waypoints=/users/cais/STUT/analysis/aparc12_tracts_2/S01/aparc12_lh_vSC.diff.txt --avoid=/users/cais/STUT/FSDATA/S01/mri/ccMask_diff.nii.gz

Sorry for the verbiage, but these are the real command lines that I use ... The waypoints file in this case is exactly the same as the stop mask. As you can see the options are exactly the same between probtrackx and probtrackx2 (pt and pt2 for short from here on).

But the results are dramatically different in one aspect: the voxel intensities inside my target mask (i.e., the waypoint and the stop mask) is very low (near zero) in the pt2 results, but very high (on the order of 1e3 - 1e4) in the pt results. It seems as if for pt2, the tracts stopped at the boundary of the target mask, whereas for pt, the tracts continued to go into it.

I wonder whether this difference between pt2 and pt is an intended new feature or improvement in pt2, or whether it is something else...

This is the version of my FSL:

amd64 (5.0.2-2, automatic)
Upgrade: fsl-atlases:amd64 (5.0.0-2, 5.0.2-2)

Thanks.

Best regards,
Shanqing


--
Shanqing Cai, Ph.D.
Post-doctoral Associate
CNS Speech Laboratory
Department of Speech, Language and Hearing Sciences
Sargent College of Health and Rehabilitation Sciences, Boston University
677 Beacon Street, Boston 02215, USA
Email: [log in to unmask]
http://people.bu.edu/scai/