diff --git a/README.md b/README.md index 2d4536f..9fa7fc0 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,7 @@ https://user-images.githubusercontent.com/2482071/227744144-ff9b21c3-d757-4e4c-a Publication linked to the dataset: https://pubmed.ncbi.nlm.nih.gov/35585865/ -Dataset: TODO - -Procedure for ground truth mask creation: https://youtu.be/KVL-JzcSRTo +Publication linked to this model: TODO (see https://github.com/ivadomed/model_seg_mouse-sc_wm-gm_t1/issues/26) ## Installation @@ -21,7 +19,18 @@ We recommend installing a [virtual environment](https://docs.python.org/3/librar pip install -r requirements.txt ~~~ -## Run segmentation +## Train model + +Dataset (internal git-annex): `zurich-mouse` + +Procedure for ground truth mask creation: https://youtu.be/KVL-JzcSRTo + +Example of training using GPU #0 and wandb group called "awesome-model" (for live monitoring): +~~~ +export CUDA_VISIBLE_DEVICES="0"; export WANDB_RUN_GROUP="GROUP_NAME"; python train.py +~~~ + +## Test model ~~~ python test.py -i NIFTI_IMAGE @@ -29,4 +38,4 @@ python test.py -i NIFTI_IMAGE ## Notes -Before running the segmentation, make sure the image orientation is correct. More details [here](https://github.com/ivadomed/model_seg_mouse-sc_wm-gm_t1/issues/25). +Before applying the model, make sure the image orientation is correct. More details [here](https://github.com/ivadomed/model_seg_mouse-sc_wm-gm_t1/issues/25).