Closed rohanbanerjee closed 5 months ago
commit a48347e0a1dd8737db70c25ca7de2923d7edd66f solves the above mentioned issues.
@MerveKaptan can you please follow the following steps and then update if the errors still persists?
1. cd fmri-segmentation
2. git pull
3. python run_inference.py --path-images <PATH_TO_IMAGE> --path-out <PATH_TO_OUTPUT> --path-model <PATH_TO_MODEL> --use-best-checkpoint -path-qc <PATH_TO_QC>
tl;dr The inference script does not currently have the compatibility for running inference on a single image. It currently works for running inference on a whole dataset.
SCT now has an nnUnetv2 wrapper, why not using it?
Oh right, that is the plan. This is a temporary script for inference. I'm in the process of making a new release with the round 2
trained model and integrate it into SCT.
This PR Adding the EPI spinal cord segmentation model to SCT adds the EPI segmentation model to SCT
Documenting the issues mentioned by @MerveKaptan in our email correspondence
tl;dr The inference script does not currently have the compatibility for running inference on a single image. It currently works for running inference on a whole dataset.