CSA Header

Parse CSA header information from Siemens MRI acquisitions with Python.

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Some Siemens MRI scans may include CSA headers that provide valuable information about the acquisition and storage of the data. These headers are stored as private data elements, usually looking something like:

(0029, 1010) CSA Image Header Type          OB: 'IMAGE NUM 4'
(0029, 1010) CSA Image Header Version       OB: '20100114'
(0029, 1010) CSA Image Header Info          OB: Array of 11560 bytes
(0029, 1020) CSA Series Header Type         OB: 'MR'
(0029, 1020) CSA Series Header Version      OB: '20100114'
(0029, 1020) CSA Series Header Info         OB: Array of 80248 bytes

The CSA Image Header Info and CSA Series Header Info elements contain encoded information which is crucial for the correct interpretation of the associated acquisition data.

For a detailed explanation on the CSA encoding scheme, please see this excellent article from NiBabel's documentation site.

Table of Contents

• Installation
• Quickstart
• Tests
• License

Installation

pip install csa_header

Quickstart

Use pydicom to read a DICOM header:

>>> import pydicom
>>> dcm = pydicom.dcmread("/path/to/file.dcm")

Extract a data element containing a CSA header, e.g., for CSA Series Header Info:

>>> data_element = dcm.get((0x29, 0x1020))
>>> data_element
(0029, 1020) [CSA Series Header Info]            OB: Array of 180076 elements

Read the raw byte array from the data element:

>>> raw_csa = data_element.value
>>> raw_csa
b'SV10\x04\x03\x02\x01O\x00\x00\x00M\x00\x00\x00UsedPatientWeight\x00      <Visible> "true" \n      \n      <ParamStr\x01\x00\x00\x00IS\x00\x00\x06...'

Parse the contents of the CSA header with the CsaHeader class:

>>> from csa_header import CsaHeader
>>> parsed_csa = CsaHeader(raw_csa).read()
>>> parsed_csa
{
    'NumberOfPrescans': {'index': 1, 'VR': 'IS', 'VM': 1, 'value': 0},
    'TransmitterCalibration': {'index': 2, 'VR': 'DS', 'VM': 1, 'value': 247.102},
    'PhaseGradientAmplitude': {'index': 3, 'VR': 'DS', 'VM': 1, 'value': 0.0},
    'ReadoutGradientAmplitude': {'index': 4, 'VR': 'DS', 'VM': 1, 'value': 0.0},
    'SelectionGradientAmplitude': {'index': 5, 'VR': 'DS', 'VM': 1, 'value': 0.0},
    'GradientDelayTime': {'index': 6,
    'VR': 'DS',
    'VM': 3,
    'value': [36.0, 35.0, 31.0]},
    'RfWatchdogMask': {'index': 7, 'VR': 'IS', 'VM': 1, 'value': 0},
    'RfPowerErrorIndicator': {'index': 8, 'VR': 'DS', 'VM': 1, 'value': None},
    'SarWholeBody': {'index': 9, 'VR': 'DS', 'VM': 3, 'value': None},
    'Sed': {'index': 10,
    'VR': 'DS',
    'VM': 3,
    'value': [1000000.0, 324.74800987, 324.74800832]}
    ...
}

Tests

This package uses hatch to manage development and packaging. To run the tests, simply run:

hatch run test

Coverage

To run the tests with coverage, run:

hatch run cov

Or, to automatically generate an HTML report and open it in your default browser:

hatch run cov-show

License

csa_header is distributed under the terms of the MIT license.