bruker2nifti package

Submodules

bruker2nifti.converter module

class bruker2nifti.converter.Bruker2Nifti(pfo_study_bruker_input, pfo_study_nifti_output, study_name=None)

Bases: object

Facade to collect users preferences on the conversion and accessing the core methods for the conversion (scan_to_struct, write_struct).

Nomenclature:

study: a series of acquisition related to the same subject, acquired in the same scanning session and usually containing multiple scans. It is provided as a folder structure containing the scans produced with paravision (PV) software. Patient/subject information are embedded in the study (opposed hierarchy as in the DICOM files).

scan or experiment, sub-scans and sub-volumes: individual folder image acquired with various protocols. To a scan can belong more than one processed image, or reconstruction. Each processed image can be a single volume or can contain more than one sub-volume embedded in the same processed image.

header: header of the nifti format.

img_data: data of the nifti format, stored in a 2d or 3d matrix.

struct: intermediate structure (python dictionary) proposed in this code, aimed at collecting the information from the raw Bruker and to progressively creating the nifti images.

convert()

To call the converter, once all the settings of the converter are selected and modified by the user. :return: Convert the Bruker study, whose path is stored in the class variable self.pfo_study_bruker_input in the specified folder stored in self.pfo_study_nifti_output, and according to the other class attributes.

Example:

>> bru = Bruker2Nifti(‘/path/to/my/study’, ‘/path/output’, study_name=’study1’)

>> bru.show_study_structure

>> bru.verbose = 2 >> bru.correct_slope = True >> bru.get_acqp = False >> bru.get_method = True # I want to see the method parameter file converted as well. >> bru.get_reco = False

>> # Convert the study: >> bru.convert()

convert_scan(pfo_input_scan, pfo_output_converted, nifti_file_name=None, create_output_folder_if_not_exists=True)
Parameters:
  • pfo_input_scan – path to folder (pfo) containing a scan from Bruker, see documentation for the difference between Bruker ‘scan’ and Bruker ‘study’.
  • pfo_output_converted – path to the folder where the converted scan will be stored.
  • create_output_folder_if_not_exists – [True] if the output folder does not exist will be created.
  • nifti_file_name – [None] filename of the nifti image that will be saved into the pfo_output folder. If None, the filename will be obtained from the parameter file of the study.
Returns:

[None] save the data parsed from the raw Bruker scan into a folder, including the nifti image.
explore_study()

Automatic filling of the advanced selections class attributes. It also checks if the given attributes are meaningful. :return:

show_study_structure()

Print to console the structure of the selected study. :return: [None] only print to console information.

bruker2nifti.open_GUI module

Module contents