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Processing

spatial normalization (registration.py)

  • antspyx
  • deep learning based spatial normalization using registration foundation model uniGradICON (https://github.com/uncbiag/uniGradICON)
  • capable of spatial normalization Amyloid PET, CT and MRI into its corresponding template in standard space (mni space)
  • implemented 1mm and 2mm istropic resolution
  • registration should be done in 1 minutes in a standard PC
  • rigid and deformative registration

segmentation (segmentation.py)

  • deep learning based segmentation using brainchop for mri t1w images (https://github.com/neuroneural/brainchop)
  • brain extraction (BET) for Amyloid PET, CT and MRI images
  • templated based segmentation optimization

harmonization (harmonization.py)

  • hoffman phantom based harmonization using EIR
  • paired MRI based harmonization using EIR
  • Combat harmonization
  • Amyloid PET enhancement using partial volume correction

Atlas

atlas management (manager.py)

  • atlas I/O
  • atlas calling API
  • atlas visualization

atlas

  • the atlas templates and masks are stored in the atlas folder
  • the atlas reading and writing is managed by manager.py (combine existing functions defined in manager.py and template.py, then remove template.py)
  • two types of spatial resolutions (1mm and 2mm)
  • template and mask covering various AD stage of amyloid PET, CT and MRI T1W

Centiloid and SUVr

  • centiloid score calculation

  • centiloid calibration

  • centiloid configuration for different sites and tracers, and its I/O API

  • tracer including C11-PIB, F18-FBP, F18-FBB, F18-FMM, F18-FBZ, and extended to new tracers

  • SUVr calculation based anatomic masks, and grouped them to larger brain regions

Reporting

  • report generation based on the atlas and centiloid score
  • report is generated from a predefined docx template, and this template is configured to be site adaptive
  • report I/O API for generation and reporting
  • report to pdf, DICOM SR
  • the report template include [Patient Information, Injection and Imaging Information, Comments, Centiloid Score, SUVr Table, Snap View of Amyloid PET in private and standard speces]
  • the report include site information in header and end.

Workflow

  • centiloid scoring workflow
  • template generation worklflow
  • calibration workflow

Utils

  • various tools
  • DICOM
  • NIFTI <> DICOM