support to write .nii files (not .nii.gz)

[samuelholly]

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.

[samuelholly]

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.

[neuronflow]

Hi @samuelholly,
thank you for your interest in BTK and for reporting back. We will look into supporting non-compressed output files.

[neuronflow]

we should also double check that reading .nii files is supported