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Stam missed something in this e-mail: 2. You don’t want to be using --invxfm if you are specifying a simple affine (use --xfm). --invxfm is only for when you specify a warpfield. In that case, you specify the forward warp with --xfm and the inverse warp with --invxfm. Correcting this should solve your problem in 3. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Xiangzhen Kong Sent: Friday, August 12, 2011 4:44 AM To: [log in to unmask] Subject: [FSL] Fw: Problems when using probtrackx [I made a mistake in the last mail and now corrected. Sorry！] Hi,all~ I came across 4 questions when using the probtrackx from FSL: 1. Will adding Waypoint masks, or Exclusion mask, or Termination mask have an effect on the value of voxels in the fdt_paths.nii.gz, if the same seed mask and target mask are used? 2. Flirt to register DWI to MRI and MRI to MNI152, and get two transformation matrix, and concat them to get a matrix M. Then I probtrackx with the option --invxfm. I want to verify if there is something wrong when adding the concated transform matrix? 3. Are the output volume fdt_paths.nii.gz is in the space of the masks? I want to confirm since my output file is not, through I saw the FSL webpage says yes. I think I may do somethin wrong, say, the problem 2. 4. How can I only get the tract connecting the seed and target mask since there are so non-zero voxels in the volume fdt_paths.nii.gz? Waiting for your valuable advice! 2011-08-12 _____ Xiangzhen Kong