brain_preprocessing

Installing the dependencies

1. Python dependencies can be installed via the dependency file requirements.txt

   pip install -r requirements.txt
   

CLI

This CLI application takes 4 structural brain MRIs (t1, t2, flair, t1ce) as input (can be either in nifti format or dicom).

python ./src/pipeline.py -h

Taking nifti files as input

python ./src/pipeline.py -t1 path/to/t1.nii.gz -t2 path/to/t2.nii.gz -fl path/to/flair.nii.gz -t1ce path/to/t1ce.nii.gz -o path/to/output/folder

Taking dicom folders as input

python ./src/pipeline.py -t1 path/to/t1/dicom/folder -t2 path/to/t2/dicom/folder -fl path/to/t1/flair/folder -t1ce path/to/t1ce/dicom/folder -o path/to/output/folder