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@@ -111,6 +111,7 @@ def split_nii_channels(nii_path, out_dir=None, flip=False, mask_index=-1, bias=F
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if i == mask_index:
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channel_data = mask_foreground(channel_data)
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+ channel_data = channel_data/np.mean(channel_data)
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new_header = nii_header
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new_header['dim'][0] = 2
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@@ -158,7 +159,6 @@ if __name__ == '__main__':
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parser.add_argument("file", help="Location of file to process")
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parser.add_argument("dir", help="Directory for preprocessed Files")
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parser.add_argument("-s", type=int, help="Series to extract")
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- parser.add_argument('-b', type=bool, default= True, help='Bias field correct image')
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parser.add_argument('--pdim', type=float, help='Pixel dimensions (Retrieved from Tiff file if not set)')
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args = parser.parse_args()
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