BraTS-Toolkit
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support to write .nii files (not .nii.gz)
Hi everyone,
first of all thank you for providing this tool to the public.
I tried to run the brats-segment
script from the command line on my Ubuntu 18.04 virtual machine:
brats-segment -t1 t1.nii -t1c t1_ce.nii -t2 t2.nii -fla flair.nii -d econib -o brats-segment-outfile.nii
However, I got the following error:
ERROR DETAIL: The outputPath is ambiguous and cannot be determined! path: brats-segment-outfile.nii, t1path: t1.nii, cid: econib
I'm inside the patient folder where all the input files are present.
Could you kindly advise how to get rid of this issue?
Thank you very much.
Hello, I managed to work-around the issue by setting the output file to be GZipped. So:
brats-segment -t1 t1.nii -t1c t1_ce.nii -t2 t2.nii -fla flair.nii -d econib -o brats-segment-outfile.nii.gz
now works.
Hi @samuelholly, thank you for your interest in BTK and for reporting back. We will look into supporting non-compressed output files.
we should also double check that reading .nii
files is supported