CorticoMetrics FreeSurfer conversion tools

Note: FreeSurfer is a set of software tools for brain segmentation of MRI data. As such, non-brain imaging applications do not apply, and the tasks defined for DICOM4QI TID1500 component cannot be addressed. However, DICOM TID1500 Strutured Reporting is applicable, and functionality is included to encode brain region volumetric statistics. Therefore, the platform is included.

  1. Description of the platform/product:

    • name and version of the software: fs2dicom v0.1.2, which works with FreeSurfer 6.0
    • free?: yes; FreeSurfer is available here, and fs2dicom is available for download from PyPI
    • commercial?: no
    • open source?: yes; FreeSurfer and fs2dicom source code are hosted on GitHub
    • what DICOM library do you use?: DCMQI to write DICOM-SR

  2. Description of the relevant features of the platform: fs2dicom incorporates the volumetric statistics created by FreeSurfer (saved as the aseg.stats file) into a DICOM SR object. These can be viewed along with the DICOM SEG object in viewers such as 3D Slicer:

  1. Read task: Not supported

  2. Write task:

    • Download the file fs2dicom-rsna2018-example-v2.tar.gz by selecting the "Download -> Direct download" menu option from here. This contains the following:
      • ./dicom-anon: Directory containting input DICOMs for a FreeSurfer-compatible T1 weighted MPRAGE sequence.
      • ./fs2dicom-rsna2018-example/fs-subjects/fs2dicom-rsna2018ex/: Directory containing the output of the above DICOMs processed with FreeSurfer 6.0 subcortical segmentations
      • fs-aseg-sr.json: File containing the volume statistics calculated by FreeSurfer, used to create the DICOM SR
      • ./aseg-sr.dcm: The DICOM SR image created by fs2dicom
      • ./aseg-seg.dcm: The DICOM SEG image created by fs2dicom, described here
      • ./readme.txt: Description of these contents, and instructions on how to run fs2dicom on the results
    • Running the example (NOTE: docker and Python >= 3.4 are required to run this. See the readme.txt and the fs2dicom GitHub page for more details):
    pip install fs2dicom   # if not installed previously
tar zxvf ./fs2dicom-rsna2018-example-v2.tar.gz
cd fs2dicom-rsna2018-example

fs2dicom create-sr \
  --aseg_dicom_seg_file ./aseg-seg.dcm \
  ./dicoms-anon/MR.1.3.12.2.1107.5.2.32.35162.1999123112191238865917962 \
  ./fs-subjects/fs2dicom-rsna2018ex/stats/aseg.stats \
  ./aseg-sr.dcm