Read data using ISMRMRD

[jcohenadad]

Alternative tools to read pfiles:

• https://github.com/njvack/pfile-tools
• https://ismrmrd.readthedocs.io/en/latest/overview.html

ISMRMRD

The ISMRMRD (International Society for Magnetic Resonance in Medicine Raw Data) library cannot directly read GE P-files (P12345.7 or similar raw data files). However, you can use additional tools or scripts to convert the GE P-file into ISMRMRD's raw data format, which is .h5.

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Steps to Work with P-files and ISMRMRD

To process P-files using ISMRMRD, you need to convert the P-file into ISMRMRD's .h5 format, as ISMRMRD is designed for a vendor-neutral raw data format.

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1. Convert P-file to ISMRMRD Format

• Using Available Tools:

  • There are converters like ge_to_ismrmrd (available in some ISMRMRD repositories or custom implementations) that can read GE P-files and write them into .h5 files compatible with ISMRMRD.
  • You may need the GE SDK (e.g., GERecon) or scripts developed by the research community to extract raw data and metadata from the P-file before conversion.

• Custom Conversion:

  • If a suitable converter is unavailable, you can write a custom script:
    1. Use GERecon or other P-file parsers to extract k-space data and metadata.
    2. Save the extracted data into ISMRMRD's .h5 format using the ISMRMRD API.

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2. ISMRMRD Workflow

Once the P-file is converted into an ISMRMRD-compatible .h5 file, you can use ISMRMRD libraries for reconstruction or processing:

Python Example with ISMRMRD:

import ismrmrd

# Open the converted ISMRMRD file
filename = "converted_file.h5"
dataset = ismrmrd.Dataset(filename, "dataset")

# Access header information
header = dataset.read_xml_header()
print(header)

# Read k-space data
for acqnum in range(dataset.number_of_acquisitions()):
    acq = dataset.read_acquisition(acqnum)
    print(acq.data)

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3. Alternative Tools

• If ISMRMRD isn't directly feasible, consider:
  • GERecon: GE-specific reconstruction software.
  • BART or custom reconstruction frameworks to handle raw k-space data extracted from P-files.
  • Third-party libraries like ismrmrd-python once you convert the file.

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Challenges

1. P-file Variants:
   • GE P-file structure may vary between scanner models or software versions. Parsing may require specific tools.
2. Conversion Requirements:
   • Access to GE SDK or reverse-engineered tools may be necessary to extract raw data.
3. Metadata Mapping:
   • Metadata in P-files might need to be reformatted to comply with ISMRMRD's conventions.

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Let me know if you’d like help with specific conversion tools or writing a custom script!