Unable to run preprocessing script

[hiaoxui]

Thanks for sharing the codebase, and congrats on acceptance!

I tried to run the preprocessing codes on the quickstart notebook on the sample NifTI file. My command is

python preprocessing/mri_preprocess_3d_simple.py \
    --temp_img ./preprocessing/atlases/temp_head.nii.gz \
    --input_dir ./data/sample/unprocessed \
    --output_dir ./data/sample/processed

The registration part runs successfully. However, an error happened for the brain extraction code:

ValueError: operands could not be broadcast together with shapes (108,137,113) (3,)

The error happens on this line (L87 of src/preprocessing/HD_BET/data_loading.py)

Do you have clues on this? Thanks!

[real-JohnYoung]

Questions happens at
"...BrainIAC/src/preprocessing/HD_BET/data_loading.py", line 87, in save_segmentation_nifti if np.any(np.array(seg_old_size) != np.array(dct['size'])[[2, 1, 0]]): ValueError: operands could not be broadcast together with shapes (108,137,113) (3,)