search

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
70 stars 11 forks source link

Preprocessor stuck on PNG slice extraction #14

Open aecelaya opened 2 years ago

aecelaya commented 2 years ago

Hi, I'm trying to use the BraTS preprocessor and it is getting stuck on the "png slice extraction" step. What could be causing the preprocessor to get stuck on this step, or is there a way to turn off this step?

Attached is the command-line output.

image

neuronflow commented 2 years ago

Thanks for your interest in btk. I have never seen a crash there, it is the very last one. Currently there is no flag to disable it. Could you elaborate on your setup? Can you process the provided example files?

aecelaya commented 2 years ago

Thank you for providing this tool. I found the issue. The Docker didn't have the necessary permissions to write to the output folder. After changing the permissions for that folder, the btk preprocessor finished running successfully.

aecelaya commented 2 years ago

A smaller issue that I'm noticing is that the Docker container outputs files whose owner is different than the current system user. Attached is a screenshot highlighting this. Is it possible to have the Docker write its output with the current user as the owner?

I'm running btk on a server with Ubuntu 20.04.2 and do not have sudo permissions to change the ownership or remove the output of btk.

image

neuronflow commented 2 years ago

Cool glad that you got it working! Thanks for reporting. We are aware of this and currently working on a fix :) follow the cryptic issue here if you want to be noticed once it is fixed: https://github.com/neuronflow/BraTS-Toolkit/issues/5