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Not quite. If your patway is saved in structural space, I would generate the mask in that very space and transform just the mask into diffusion space (reference space would be diffusion, or the nodif-image). Check which image is in which space in fslview. Good luck- Cheers, Andreas ________________________________ Von: FSL - FMRIB's Software Library im Auftrag von Kristen Lindgren Gesendet: Mo 02.01.2006 19:07 An: [log in to unmask] Betreff: Re: [FSL] AW: [FSL] AW: [FSL] Calculating FA after probabilistic tractograp hy Thanks, Andreas. That's a good point. I didn't think of that. So in the ApplyXFM_gui, I should use str2diff.mat as the transformation matrix with anat as the reference volume and just enter fdt_paths as the input volume, right? Thanks for the input! Kristen -----Original Message----- From: FSL - FMRIB's Software Library To: [log in to unmask] Sent: 1/2/2006 12:58 PM Subject: [FSL] AW: [FSL] AW: [FSL] Calculating FA after probabilistic tractograp hy Hi, why don't you want to proceed the other way around, i.e. transform the mask into diffusion space by the inverse of diff2str.mat)? If you transform the FA map, the interpolation may alter your FA values whereas getting a binary mask in diffusion space should be straight forward. Cheers- Andreas ________________________________ Von: FSL - FMRIB's Software Library im Auftrag von Kristen Lindgren Gesendet: Mo 02.01.2006 17:58 An: [log in to unmask] Betreff: Re: [FSL] AW: [FSL] Calculating FA after probabilistic tractograp hy Hello. I have a quick follow-up question to your instructions on how to calculate FA from probabilistic tractography. In previous e-mails, I was told to use the following commands to get this information: avwmaths_32R pathway -thr <threshold> -bin -mul dti_FA FAmask avwstats FAmask -M However, I just realized that my masks for probabilistic tractography (mode=twomasks_symm) were in anatomical space and not diffusion space; therefore, I had to apply the diff2str.mat transform during probtrack. Does this mean that I need to apply the diff2str.mat transform to dti_FA before using the above commands? If so, are these the selections I would make? Transformation matrix = diff2str.mat Input volume = dti_FA Reference Volume = anat (T1 image that was used for registration), based on existing volume Thanks for your help. Hope you had a great holiday! Kristen