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What is the output when you type fslorient <file that would be swapped by fslview>. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Leonardo Cerliani Sent: Friday, November 07, 2008 5:24 AM To: [log in to unmask] Subject: [FSL] (unwanted) X swap when saving nii.gz reconstructed from PAR/REC 4.1 hello everyone! I am experiencing a strange (and potentially dangerous) behavior when saving nii.gz files (modified or not) from fslview 3.0: the image is swapped on the X axis. (I don't know if it can mean something, but I have no such problem when performing operations with fslmaths on the same image.) Did some of you experienced the same problem? The images have been reconstructed in nii.gz from PAR/REC 4.1 files by means of the dcm2nii commandline utility contained in MRIcroN. One interesting thing: if I use the fslchfiletype utility to convert the nii.gz to analyze, and then back to nii.gz, then I can open/modify/save with fslview, and everything is alright. I suspect therefore that it could be some problem with the header generated by dcm2nii (which actually if I remember well doesn't still fully support PAR/REC 4.1) P.S. By the way, if some of you knows some other tool to reconstrut PAR/REC files, it would be very welcome. system specifications: linux opensuse 10.2 fsl 4.0 fslview 3.0 leonardo