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Hi, I am helping a student segment fetal images. The images have been manually coregistered to a fetal MNI template corresponding to the correct gestation week (Computational Radiology Laboratory - Fetal Brain Atlas). This atlas also provides tissue prior maps. Running FAST from the FSL gui, I specify the priors for both parts of the calculations (-A option in the command line). The resulting pve images look pretty good considering the quality of the input data. However, the standard space GM, WM, and CSF maps bear no relation to the native space of the either the input images or the tissue priors. I realize this is because FAST defaults to using the FLIRT schedule for registration into standard, 'adult' MNI space. I have tried using FLIRT to calculate my own .mat file from the manually coregistered fetal images to the fetal MNI template, however, the resulting transform is really bad (incorrect voxel size, image origin, image orientation, FOV, etc.), especially considering that the input image and the template image were manually coregistered before hand. Is there a way to bypass this registration step in FAST? I couldn't really find anything on either the message boards or in the FAST wiki. Thanks, suzanne ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1