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TotalSegmentator method added in volume.from_nifti() #77

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Update volume.py
wu-qiyuan Jun 3, 2022
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Update Readme.md
Zhiyuan-Ding authored Jun 5, 2022

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commit ebab61688eaadd48a0948e8f99513f72f79930ee
2 changes: 1 addition & 1 deletion ct-org/Readme.md
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@ CT-ORG is a 5-classes abdominal organ segmentation model as in [CT-ORG, a new da

## Mask generation steps
1. Installing the pre-trained models from [previous link](https://github.com/bbrister/ct_organ_seg_docker).
2. Running org_mask_batch.py.(Currently I/O part still in in file for modification, before publication this should be worked in command line format).
2. Running `org_mask_batch.py`.(Currently I/O part still in in file for modification, before publication this should be worked in command line format).
3. In some cases the original docker setting up will not work due to the following reasons:
- For issues with CPU/GPUs, add `--gpus gpu_index` in ./docker/run_docker_container.py line `sudo docker run --gpus all -v $HOST_SHARED:$CONTAINER_SHARED -t $IMAGE $INFILE $OUTFILE`
- For issues with `IOError: CRC check failed`, this is due to `nibabel` or nii data version, change `get_data` to `get_fdata`.