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Hi, If you cannot get FNIRT to work with 2D data then you could try a work-around which was to build a 3D image from repeated copies of the same 2D slice. You can then extract a 2D result (image or warpfield) by taking out the central slice from the fake 3D image. All the best, Mark On 26 Nov 2013, at 19:29, Dr. András Jakab <[log in to unmask]> wrote: > Dear FSL list, > > Is it somehow possible to use FNIRT for registering 2D images (MRI file but only one slice, cardiac)? Apparently it does not work this way by default. > > Thank you. > Regards, > András > - > -- > Dr. med. Andras Jakab, MD. PhD. > Marie Curie Post Doctoral Research Fellow > Computational Image Analysis and Radiology Lab > Medizinische Universität Wien > Universitätsklinik für Radiologie und Nuklearmedizin > Währinger Gürtel 18-20 > A-1090 Wien > Cellular: +36305095083 > ----------------------------------