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a guest May 22nd, 2019 68 Never
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  1. from nipype.interfaces.dcm2nii import Dcm2niix
  2. from tempfile import mkdtemp
  3. import sys
  4.  
  5.  
  6. def main():
  7.     dcmpath = sys.argv[-1]
  8.     outdir = mkdtemp()
  9.  
  10.     # interface
  11.     x = Dcm2niix()
  12.     x.inputs.source_dir = dcmpath
  13.     x.inputs.bids_format = True
  14.     x.inputs.output_dir = outdir
  15.  
  16.     print(outdir)
  17.     res = x.run()
  18.  
  19.     import pdb; pdb.set_trace()
  20.  
  21. if __name__ == "__main__":
  22.     if len(sys.argv) != 2:
  23.         print("Provide DICOM directory path")
  24.         sys.exit(1)
  25.     main()
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