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Hello FSL community, I have been following the instructions posted on the FSL web pages for Freesurfer & FSL Interoperation (which have been very useful!). We primarily use AFNI, although we are currently using several of the FSL utilities such as BET and flirt. I am a relatively new user to Freesurfer. I have successfully created structural datasets in Freesurfer, including final surfaces, and I am attempting to overlay functional activation on these surfaces. Using mri_convert, I have created an analyze version of the Freesurfer Pre-processed structural (T1). I have also created an analyze version of a functional volume for the same subject (through AFNI). Here is where the problem arises: I am using flirt to register this functional volume to the Freesurfer preprocessed structural T1, as indicated, but I am getting a "segmentation fault" from Flirt. A dumb question, but, what are some of the reasons that Flirt might seg fault with this data? Here are some of the things I do know to be true about this data: 1)I use flirt quite often, so I know that it must be something about my data that is causing the problem. I am suspecting it is the (analyze) FS-pre-processed structural T1. 2) both datasets are in coronal slice order 3) both datasets can be viewed in an analyze image viewer (MRICro), and look fine 4) the functional volume CAN register to itself using Flirt 5) the analyze T1 from Freesurfer CANNOT register to itself using Flirt(seg fault) here is my flirt command line: flirt -in funcvol.hdr -ref struc_fs_T1.hdr -v -searchrx -180 180 -searchry -180 180 - searchrz -180 180 -out func_reg_to_FST1 -omat funcreg_to_fst1.mat Hopefully, someone may be able to shed some light on this problem, and offer a possible solution. Thanks in advance, Tim Souza