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FreeSurfer certainly has a segmentation that you can use, since I don't use the segmentation directly from FreeSurfer, rather I generate it in Caret from the FreeSurfer white matter surface, I don't know the exact file you should use. You can simply mask the tractography result with the FreeSurfer segmentation in fslmaths (or even in fslstats). Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Lindgren, Kristen, Ann Sent: Saturday, March 28, 2009 7:20 PM To: [log in to unmask] Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths Matt, quick follow-up question. You had mentioned in a previous e-mail that instead of thresholding FA it would be more appropriate for me to confine my thresholded masks within a white matter segmentation. I was thinking that I could use the white matter segmentation from freesurfer (one for each hemisphere) for this. Any ideas on how I could do this? Is it something I could do within fslmaths or is it something I'd need to define when I run probtrackx? Thanks! Kristen -----Original Message----- From: FSL - FMRIB's Software Library on behalf of Matt Glasser Sent: Sat 3/28/2009 7:48 PM To: [log in to unmask] Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths Well, I draw the ROI on the cortical surface in Caret and then map it to the volume, which makes a 1 voxel thick ROI in the voxels of the white matter surface. There are a number of ways to generate the white matter surface, however. Before I started using freesurfer, I used the FAST segmentations. I took the white matter mask from FAST, blurred it with a 3x3x3 voxel kernel, and then selected voxels with values between .50 and .85. This produced a white matter surface ribbon that is about 1 voxel thick. You could then find the intersection between your ROI and the ribbon to get the cortical ROI that is only in the first white matter voxel. I always correct for distortions (there are a variety of ways to do this, a phase up/phase down correction is best, but you can also use a field map or even use FNIRT to register your FA to your T1 and then apply the warpfield to your raw data). The issues I describe below occurred from tractography from ROIs in diffusion space. It is worse in some brains, or acquisitions than others, but I just choose to avoid it across all subjects, rather than make exclusion/termination masks on a case by case basis. I am not convinced that you get more information by tracking into the cortical grey matter, given the resolution of DTI, than you get from tracking up to the superficial white matter, and you can avoid errors this way. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Martin Kavec Sent: Saturday, March 28, 2009 7:36 AM To: [log in to unmask] Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths Hi Matt, On Fri, Mar 27, 2009 at 10:54 PM, Matt Glasser <[log in to unmask]> wrote: I always track from white matter. If it is a cortical ROI I use the 1st voxel of the white matter surface. That's an interesting approach. How do you get from cortical ROI to the 1st voxel of the WM? Honestly, I have found that tracking from/into cortical grey matter results in more error than useful information (its easy to get pathways crossing sulci for example, if you combine partial voluming with the fact that the principle diffusion direction in cortical grey matter is oriented perpendicular to the cortical surface, and cortical grey matter ROIs may be very close to brain rim voxels). Could this simply be because of the nonlinear distortions between DTI and FreeSurfer input image? It could be several voxels in most of the brain. Thanks, Martin