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Hi Natalie Not sure if you need to do anything if the masks you edited are named as *_FA_mask.nii.gz. If not so, then you can either name it so that it is *_FA_mask.nii.gz or edit $FSLDIR/bin/fsl_reg so that the correct naming convention of your choice gets picked up as weight-masks. Best, Danny Kim ________________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Natalie Busby [[log in to unmask]] Sent: Wednesday, February 24, 2016 6:09 AM To: [log in to unmask] Subject: [FSL] tbss_2_reg script edit Hi, I am trying to use TBSS on stroke patients with large lesions. I have edited the masks created in the tbss_1_preproc stage to avoid the lesions. However I am unsure how to edit the tbss_2_reg script to incorporate these masks. Sorry - a newbie to tbss and scripting in general so some basic instructions would be useful! Best wishes, Natalie