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neuronflow / BraTS-Toolkit

Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
https://www.frontiersin.org/articles/10.3389/fnins.2020.00125/full
GNU Affero General Public License v3.0
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support to write .nii files (not .nii.gz) #18

Open samuelholly opened 1 year ago

samuelholly commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

neuronflow commented 8 months ago

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