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/processedThe 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!
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/processedThe registration part runs successfully. However, an error happened for the brain extraction code:
The error happens on this line (L87 of
src/preprocessing/HD_BET/data_loading.py)Do you have clues on this? Thanks!