Merge pull request #44 from ivadomed/jv/segment_sc_using_contrast_agnostic_model

Segment SC using contrast agnostic model

Author: valosekj

segment_sc_contrast-agnostic/README.md

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+Segment SC using contrast-agnostic MONAI model from PSIR contrast and perform vertebral labeling
+
+1. Create a conda virtual environment and install dependencies
+
+```console
+yes | conda create -n monai python=3.9
+conda activate monai
+yes | pip install -r segment_sc_contrast-agnostic/requirements.txt
+```
+
+2. Segment SC using the contrast-agnostic MONAI model from PSIR contrast and perform vertebral labeling
+
+The `sct_run_batch` wrapper script is used to run the `segment_sc_contrast-agnostic/segment_sc_contrast-agnostic.sh` across multiple subjects in parallel.
+
+```console
+sct_run_batch -config config.json
+```
+
+Example `config.json` file:
+
+```json
+{
+  "path_data"   : "<PATH_TO_DATASET>/canproco",
+  "path_output" : "<PATH_TO_DATASET>canproco_contrast-agnostic_2023-10-06",
+  "script"      : "${HOME}/code/canproco/segment_sc_contrast-agnostic/segment_sc_contrast-agnostic.sh",
+  "jobs"        : 1,
+  "include"     : "ses-M0",
+  "exclude_list": "sub-mon118 sub-mon006 sub-mon009 sub-mon032 sub-mon097 sub-mon148 sub-mon168 sub-mon191 sub-van176 sub-van206 sub-tor133 sub-cal149",
+  "script_args" : "${HOME}/code/canproco/segment_sc_contrast-agnostic/run_inference_single_image.py ${HOME}/data/models/contrast-agnostic_final_monai_model/nnunet_nf=32_DS=1_opt=adam_lr=0.001_AdapW_CCrop_bs=2_64x192x320_20230918-2253"
+}
+```
+
+ℹ️ The `exclude_list` is a list of subjects to exclude from the batch processing. It is based on the https://github.com/ivadomed/canproco/blob/main/exclude.yml file.
+
+ℹ️ The conda environment with MONAI is required to run the `segment_sc_contrast-agnostic/segment_sc_contrast-agnostic.sh` script.
+
+ℹ️ Note that the `segment_sc_contrast-agnostic/run_inference_single_image.py` script is just a copy of the 
+[`contrast-agnostic-softseg-spinalcord/monai/run_inference_single_image.py`](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/nk/monai/monai/run_inference_single_image.py) script.
+

segment_sc_contrast-agnostic/requirements.txt

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+dynamic_network_architectures==0.2
+joblib==1.3.0
+loguru==0.7.0
+monai[nibabel]==1.2.0
+scipy==1.11.2
+numpy==1.24.4
+--extra-index-url https://download.pytorch.org/whl/cpu
+torch==2.0.0