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Hi, I have not seen this before and it should not happen as FSLOUTPUTTYPE determines the output, which will be consistent for all tools. Is it possible that you double-clicked on one of the files while the script was running? Or, alternatively, did you do something with the files between the first run and a subsequent run of the script? Opening/double-clicking the files can cause the OS to unzip the file (converting a .nii.gz to a .nii) and then you get this error. If the above does not explain it, and you consistently get this error, then let us know more details. All the best, Mark On 24 Nov 2012, at 13:22, Jiyang Jiang <[log in to unmask]> wrote: > Dear FSLers, > > when running fsl_anat, we had the following error message: > > $ fsl_anat -i tmp > Fri Nov 23 23:05:57 EST 2012 > Reorienting to standard orientation > Fri Nov 23 23:06:01 EST 2012 > Automatically cropping the image > > > > WARNING!!!! Multiple image files detected: > T1_fullfov.nii T1_fullfov.nii.gz > > STOPPING PROGRAM > Could not open matrix file T1_nonroi2roi.mat > Cannot read input-matrix > =============================== > under the tmp.anat directory: > $ ls > log.txt T1_fullfov.nii.gz T1_fullfov.nii T1_orig.nii T1_std2orig.mat > T1_fullfov.nii T1_orig2std.mat T1_roi.log > > > There are indeed two files having the same name T1_fullfov.nii and T1_fullfov.nii.gz. > > The contents of the log.txt file: > > Script invoked from directory = /data/public/tmpRun > Output directory = tmp.anat > Input image is tmp > > /share/apps/fsl/5.0.1/bin/imcp T1 T1_orig > /share/apps/fsl/5.0.1/bin/fslreorient2std T1 > /share/apps/fsl/5.0.1/bin/convert_xfm -omat T1_std2orig.mat -inverse T1_orig2std > .mat > /share/apps/fsl/5.0.1/bin/fslreorient2std T1 T1 > /share/apps/fsl/5.0.1/bin/immv T1 T1_fullfov > /share/apps/fsl/5.0.1/bin/robustfov -i T1_fullfov -r T1 -m T1_nonroi2roi.mat > /share/apps/fsl/5.0.1/bin/convert_xfm -omat T1_roi2nonroi.mat -inverse T1_nonroi > 2roi.mat > > What is the problem? Thank you very much. > > Rgds, > Jiyang >