hi –
It looks like you are running this on our sample data. We use those data routinely to test for cross-platform consistency, so we haven’t encountered this issue.
I do see some differences in the inputs between the two calls you make.
Your file on the linux line is named “/home/wayne/Desktop/mrtest2/2523412.dwi.bfc.nii.gz “, but the call in Windows uses 2523412.bfc.nii.gz. What is /home/wayne/Desktop/mrtest2/2523412.dwi.bfc.nii.gz? Is it the same as 2523412.bfc.nii.gz or did you apply bfc to the dwi data?
The other difference I see is 2523412.dwi.nii.gz vs 2523412.dwi.nii, but that shouldn’t affect anything unless the files don’t match.
thanks,
David