ITK Release 4/Data Collection

Overview

Testing Data

• Testing Data
  • (Slides Set 1:PPT,ODP,PDF)
  • (Slides Set 2: )

MIDAS Structure

• Communities (recursive)
  • Collection
    • Items
      • Resources
        • Bitstreams
      • Bitstreams

Expected Data

• Maintain data using original acquisition format (Bill's suggestion)?

Group	Expected Amount of Data	File Formats	Features
Raghu Machiraju	10 Gb	TIFF, LSM, MetaImage
Ziv Yaniv	10 Gb	DICOM, MetaImage (e.g. segmentation label maps), bmp/jpg/avi (2D frame grabbed US and x-ray fluoroscopy images)
Brad Lowekamp	10 Gb	TIFF ?
Hans Johnson	4 Gb	GE45, Phillips, Siemens, Dicom, Analyze, Nifti, etc Migration from : http://www.nitrc.org/projects/brainstestdata/	Dictionary of expected meta-information (spacing, size, data-type, etc)
Sean Megason	10 Tb	TIFF, LSM File:Megason-A2D2proposal-SCORExx.pdf
Marcel Pratwsaw	10 Gb	??
Marc Niethammer	10 Gb	TIFF	Point spread functions (and image, or 12 (key,value) pair parameters

MetaData

Medical

• physical quantities associated with image acquisition apparatus (e.g. camera calibration for endoscopy and x-ray, US calibration).
• reason for scan (e.g. suspected liver tumor), should be in header but often is not.
• contrast phase (e.g. pre contrast, arterial phase).
• respiratory phase (e.g. end inspiration, end expiration).
• apparatus used to acquire images when not specified in DICOM (e.g. xyz frame grabber).
• rigid transformation data acquired with a tracker (pose of US/endoscope relative to tracking system, required for positioning multiple 2D images in 3D space)
• calibration data of other equipment used in experiment (calibration of tracked pointer)

Structure

Suggested Organization

Strawman of data organization

Filename scheme

  AllSubjects/Subject/ScanDateTime/Modality/Subject_ScanDate_Modality.nii.gz

ScanDate is in the form YYYYMMDDTT where we only keep 2 digits of time.

so you would have e.g.

 ITKTestCTdata1/0001/2010122200/T1/0001_2010122200_T1.nii.gz

MIDAS Installations

• http://www.insight-journal.org/midas/
  • http://www.insight-journal.org/midas/community/view/22 (Miscellaneous collection of ITK related data)
• http://www.insight-journal.org/rire/ (RIRE: Retrospective Registration Evaluation)
  • http://www.insight-journal.org/midas/community/view/16
• http://midas.kitware.com/
  • http://midas.kitware.com/community/view/7 (ITK Testing Data)
  • http://midas.kitware.com/community/view/22 (Tutorials: Virtual Appliances > 2Gb)

Integration with CTest

• http://review.source.kitware.com/#change,301
• http://www.kitware.com/midaswiki/index.php/MIDAS%2BCTest

BrainWeb Datasets

• http://mouldy.bic.mni.mcgill.ca/brainweb/
• http://midas.kitware.com/collection/view/44

XNAT

• http://central.xnat.org/app/template/Index.vm

Data Licenses

• http://www.kitware.com/blog/home/post/72
  • Public Domain Dedication and License (PDDL) — “Public Domain for data/databases” http://www.opendatacommons.org/licenses/pddl/
  • Attribution License (ODC-By) — “Attribution for data/databases” http://www.opendatacommons.org/licenses/by/
  • Open Database License (ODC-ODbL) — “Attribution Share-Alike for data/databases” http://www.opendatacommons.org/licenses/odbl/

• Designed by the Scientific Commons at http://www.opendatacommons.org/