<reponame>tsmonteiro/fmri_proc
import os
import argparse
import nibabel as nib


parser = argparse.ArgumentParser(description='Deepbrain skull stripping')

reqoptions = parser.add_argument_group('Required arguments')
reqoptions.add_argument('-i', '-in', dest="img_path", required=True, help='T1 Image' )
reqoptions.add_argument('-o', '-out', dest="out_path", required=True, help='Brain Mask Path' )

args = parser.parse_args()

img_path  = args.img_path
outFile = args.out_path



# Load a nifti as 3d numpy image [H, W, D]
img = nib.load(img_path)

nib.save(img, outFile)

import os
import argparse
import nibabel as nib


parser = argparse.ArgumentParser(description='Deepbrain skull stripping')

reqoptions = parser.add_argument_group('Required arguments')
reqoptions.add_argument('-i', '-in', dest="img_path", required=True, help='T1 Image' )
reqoptions.add_argument('-o', '-out', dest="out_path", required=True, help='Brain Mask Path' )

args = parser.parse_args()

img_path  = args.img_path
outFile = args.out_path



# Load a nifti as 3d numpy image [H, W, D]
img = nib.load(img_path)

nib.save(img, outFile)
# Load a nifti as 3d numpy image [H, W, D]