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I just used the defaults in the FDT GUI (other than changing Number of Samples to 100). Here's the command that was used for case (2): /export/fsl-5.0.1/bin/probtrackx2 -x /BlueArc-scratch/mharms/REWARD/bedpostx/myT halMask.nii.gz -V 1 -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 100 --fibthresh=0.01 --distthresh=0 --sampvox=0.0 --xfm=/BlueArc-scratch/mharms/REWA RD/bedpostx/RW1001.bedpostX/xfms/standard2diff.mat --forcedir --opd -s /BlueArc- scratch/mharms/REWARD/bedpostx/RW1001.bedpostX/merged -m /BlueArc-scratch/mharms /REWARD/bedpostx/RW1001.bedpostX/nodif_brain_mask --dir=/BlueArc-scratch/mharms/ REWARD/bedpostx/RW1001.probtrackx.WayFrontal --waypoints=/BlueArc-scratch/mharms /REWARD/bedpostx/RW1001.probtrackx.WayFrontal/waypoints.txt --waycond=AND thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask] From: Matt Glasser <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Friday, December 7, 2012 1:18 PM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] waytotal relationship of Waypoint vs. Exclusion Masks Can you post your probtrackx line? Are you sure you are tracking in only one direction? Thanks, Matt. From: Michael Harms <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Friday, December 7, 2012 1:07 PM To: <[log in to unmask]> Subject: Re: [FSL] waytotal relationship of Waypoint vs. Exclusion Masks And to add a 4th situation that I just tried: 4) If I use the same frontal ROI as a Classification Target (and no other target masks) and then sum the total of the entries in the resulting seeds_to_FrontalLobe.nii.gz file, I got 19352, which is in the ballpark of the value from case (2), but not identical. Why not? (I was expecting that the Classification Targets would basically function as Waypoint masks as regards the sum total of the values in the seeds_to_XXXX output). Hello, I was hoping someone could quickly explain the following. Say I have a Thalamic seed mask with 1156 voxels, and I run probtrackx with Number of samples = 100 1) If I use no Target, then I get waytotal = 115600, which makes sense (1156*100) 2) If I use a Waypoint mask of a frontal ROI, I got waytotal = 18025 3) If I use that same frontal ROI as an Exclusion mask (and no other target masks) I got waytotal = 115262 Why is it that the waytotal values for (2) and (3) don't sum to 115600? Or stated differently, I interpret (2) as indicating that 18025 streamlines hit the frontal ROI at some point but (3) seems to indicate that only 115600 - 115262 = 338 streamlines got excluded for hitting the frontal ROI when I used it as an exclusion mask. thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask]