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Sample in-utero Fetal Brain MRI DICOMs in Orthanc

This repository contains scripts for downloading a dataset of in-utero fetal brain T2-weighted MRI data, converting it to DICOMs, and using Orthanc to add fake patient and study metadata.

The intended use is for testing https://github.com/FNNDSC/fetal-recon-ui-mvp

The source data is publicly available data from https://github.com/bchimagine/fetal-brain-extraction_t2w

Output

Running all the scripts produces 3 patients in Orthanc, each with one study. All patient data (PatientID, PatientName, PatientName, PatientBirthDate, PatientAge) are fake and random.

The studies are called:

  • Fetal Neuro Indications
  • Fetal Neuro Indications
  • EI Fetal Neuro

All three studies have the same data. The SeriesDescriptions are:

  • 3 PLANE LOC
  • 3 PLANE LOC
  • CERVIX T2 HASTE PRE SCAN( RUN COR AND SAG TO MOM) (UTERUS)
  • CERVIX T2 HASTE with prescan ON
  • EPI_highres_with_distortion
  • EPI_highres_with_distortion_MoCo
  • FUJI Basic Text SR for HL7 Radiological Report
  • FUJI Presentation State - ANNOTATIONS
  • GEechoes3_EPI_SMS2_GRAPPA2_Echo_0
  • GEechoes3_EPI_SMS2_GRAPPA2_Echo_1
  • GEechoes3_EPI_SMS2_GRAPPA2_Echo_2
  • T2 FETAL Uterus
  • T2 FETAL Uterus
  • T2 FETAL Uterus
  • T2 HASTE 4 concat short TR
  • T2 HASTE 4 concat short TR
  • T2 HASTE 4 concat short TR
  • TRUFISP-BRAIN
  • TRUFISP-BRAIN
  • TRUFISP-BRAIN
  • TRUFISP-BRAIN
  • TRUFISP-BRAIN-first scan PRESCAN ON

Every series containing the word "T2" contains a fetal brain MRI stack. Other files do not contain PixelData.

Usage

# clone this repository
git clone https://github.com/FNNDSC/fetal_t2mri_dicoms.git
cd fetal_t2mri_dicoms

# download NIFTI data, convert to DICOM, and create fake DICOMs
./download_and_dicomize.sh

# upload to a local Orthanc (w/o authentication)
./upload2orthanc.sh

# add metadata and create copies of datasets in Orthanc
node modifyInOrthanc.js