dicom2nifti.convert_dicom module

dicom2nifti

@author: abrys

class dicom2nifti.convert_dicom.Vendor

Bases: object

Enum with the vendor

GE = 2

GENERIC = 0

HITACHI = 4

PHILIPS = 3

SIEMENS = 1

dicom2nifti.convert_dicom.are_imaging_dicoms(dicom_input)

This function will check the dicom headers to see which type of series it is Possibilities are fMRI, DTI, Anatomical (if no clear type is found anatomical is used)

Parameters:dicom_input – directory with dicom files or a list of dicom objects

dicom2nifti.convert_dicom.dicom_array_to_nifti(dicom_list, output_file, reorient_nifti=True)

Converts dicom single series (see pydicom) to nifty, mimicking SPM

Examples: See unit test

will return a dictionary containing - the NIFTI under key ‘NIFTI’ - the NIFTI file path under ‘NII_FILE’ - the BVAL file path under ‘BVAL_FILE’ (only for dti) - the BVEC file path under ‘BVEC_FILE’ (only for dti)

IMPORTANT: If no specific sequence type can be found it will default to anatomical and try to convert. You should check that the data you are trying to convert is supported by this code

Inspired by http://nipy.sourceforge.net/nibabel/dicom/spm_dicom.html Inspired by http://code.google.com/p/pydicom/source/browse/source/dicom/contrib/pydicom_series.py

Parameters:

• reorient_nifti – if True the nifti affine and data will be updated so the data is stored LAS oriented
• output_file – file path to write to
• dicom_list – list with uncompressed dicom objects as read by pydicom

dicom2nifti.convert_dicom.dicom_series_to_nifti(original_dicom_directory, output_file=None, reorient_nifti=True)

Converts dicom single series (see pydicom) to nifty, mimicking SPM

Examples: See unit test

will return a dictionary containing - the NIFTI under key ‘NIFTI’ - the NIFTI file path under ‘NII_FILE’ - the BVAL file path under ‘BVAL_FILE’ (only for dti) - the BVEC file path under ‘BVEC_FILE’ (only for dti)

IMPORTANT: If no specific sequence type can be found it will default to anatomical and try to convert. You should check that the data you are trying to convert is supported by this code

Inspired by http://nipy.sourceforge.net/nibabel/dicom/spm_dicom.html Inspired by http://code.google.com/p/pydicom/source/browse/source/dicom/contrib/pydicom_series.py

Parameters:

• reorient_nifti – if True the nifti affine and data will be updated so the data is stored LAS oriented
• output_file – file path to write to if not set to None
• original_dicom_directory – directory with the dicom files for a single series/scan

:return nibabel image