Closed naga-karthik closed 11 months ago
@naga-karthik is this PR ready for use/review? We have a collaborator in Berlin who has challenging 7T images and I'd like to give this contrast-agnostic model a try
Hey @jcohenadad, yes the PR is ready. We will be merging it this week. Meanwhile, the inference script is also ready to use.
For --chkp-path
please use
/home/GRAMES.POLYMTL.CA/u114716/duke/projects/ivadomed/contrast-agnostic-seg/models/monai
as the model is currently stored there
I'm having issues installing the deps:
I'm having issues installing the deps:
I had the same issue on my local macboook, I had to remove packages versions; see updated requirements from canproco repo.
Then I ran:
conda create -n monai python=3.8
conda activate monai
pip install -r requirements.txt
I'm having issues installing the deps:
I had the same issue on my local macboook, I had to remove packages versions; see updated requirements from canproco repo.
Then I ran:
conda create -n monai python=3.8 conda activate monai pip install -r requirements.txt
Thank you @valosekj -- there see to be some confusion about Python's version: https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/pull/60/files#diff-45765be45b87970b013c24cdb66c4f4ad139e802f0f013e0bbf56ecf249478eeR12
I have another error with python 3.8:
same issue when targetting requirements.txt
instead of requirements_inference.txt
@jcohenadad can you try installing the dependencies now? I think the +cpu
in torch package was causing the issue. I removed it in latest commit.
Please stick to python=3.9
as my code is based on 3.9
. (however, for simply running the inference script, the python versions shouldn't matter much, as we're using basic python commands. But using 3.9
will keep it consistent with the rest of the monai code)
2e3528269754b30986e636b45e57bfe51df1b1fb fixed it 🎉
I understand the benefits in duplicating code to isolate other projects (eg https://github.com/ivadomed/canproco/pull/44/files), but it comes at a cost of a lack of testing/feedback from the team. I strongly suggest to keep only one codebase/documentation, and iterate on that codebase/documentation.
@jcohenadad can you try installing the dependencies now? I think the
+cpu
in torch package was causing the issue. I removed it in latest commit.Please stick to
python=3.9
as my code is based on3.9
. (however, for simply running the inference script, the python versions shouldn't matter much, as we're using basic python commands. But using3.9
will keep it consistent with the rest of the monai code)
Working for me as well! Thanks! I updated the canproco files in https://github.com/ivadomed/canproco/pull/44/commits/688d1a0f99f98171825644da4bf5d5c972be38c6 to be in line with this PR.
merging to Sandrine's branch -- discussed in the internal meeting
This PR adds all the required scripts for bids-msd dataset conversion, training and running inference with MONAI models.