Dear FSL experts,
I'm trying to create a transformation matrix to use for probabilistic tractography (data processed with bedpostX). The transformation from structural space to diffusion space was not perfect, so I used nudge to optimize the alignment. I then retrieved the output transformation matrix from /tmp, which has has .xfm extension. I'd like to concatenate it with the initial transformation from flirt (.mat extension). I've tried a few things and I can't get convert_xfm to read the .xfm file (I continue to get the error "Could not open matrix file nudge_..." "Cannot read input-matrix", even when I copy the file contents into the .mat file and resave, for example). As this transformation matrix was created in FSL, I expect that there is a way to work with it, and am guessing there will be a quick easy fix, but I couldn't find an answer to this specific problem on the forums. Any help would be much appreciated!
Best wishes,
Jessica
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