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Dear Anna I think you could following the following manual of how to perform fiber tractogaphy using TBSS based ROI http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide#Transforming_TBSS_results_back_to_native_space Best Paul > Date: Wed, 22 May 2013 22:57:24 +0100 > From: [log in to unmask] > Subject: [FSL] tract-based seeds for probtrackx2? > To: [log in to unmask] > > Hi all, > > I'm getting set up for running probtrackx2 on a number of subjects, and I would like to define my seeds and targets in "tbss space", for lack of a better word. What I mean by that is: I'd like to pick an ROI on the mean_FA_skeleton, and when that gets projected into diffusion space, I'd like it to be projected to the corresponding tract center of the individual subject (i.e. where the values for the all_FA_skeletonised 4D dataset were drawn from). > > From the way I understand tbss, this is not the same place in diffusion space where I would end up if I simply registered my bedpostx diffusion data with the standard FMRIB_FA brain. Even though I warped everybody's FA to that brain in tbss_2_reg, I then used the -S option for tbss_3, which in itself would make my study-specific mean_FA image differ from the FMRIB_FA, and the tract-center search step in tbss_4 makes me end up in yet a different place. Yet that latter place seems to be the one I want to track from, because only in that case I can be sure that I track from each individual's tract center. > > Is this possible? Theoretically, all necessary transformations should be stored somewhere after the tbss, correct? And if it's not, what is the closest I can get with the available options? > > Thanks so much! > Anna