Date

(every other week)

Attendees

  • T Nolan (present)

  • Aaron (present)
  • Jonathan (present)
  • Tuhin (present)
  • Lakshmi
  • Linda (present)
  • Kirk (present)
  • Fred 
  • Phil
  • Bill (present)
  • Quasar
  • Jeff
  • Terri
  • Sohrab (present)

Goals

  • Stand up a wiki
    • get everyone on the team into Confluence and into this Space
  • Set goals
  • Plan next steps toward achieving goals

Discussion items

TimeItemWhoNotes

infrastructure: 

hardware

software


  • import from <places> into Posda then into NBIA
  • There is a hangup between SECTRA to Posda-to-ARIES
  • Cancerimagingarchive.net has a landing page (Wordpress, Confluence, NBIA-for-search-and-download)


MongoDB to manage nonDICOM data?

  1. What processes <are, should be> built?
  2. JSON IS DECIDED as the right standard format to feed MongoDB 
    1. Potentially, in addition, CSV for tabular data (Posda understands DICOM, JSON, CSV)
    2. how to handle embedded formulae in excel multitabular data for example will be a Posda feature
  3. Annotation based on this type of file format?
  4. Potential descriptions from the PI for each column on a form
  5. What does search mean - which data elements are Posda cleaning versus which pieces are Posda Harmonizing
  6. Deale neuropsych ontology; Poldrack ontology?



Collection 1: Gait and PDTuhin
  1. Linkage between ARIES ID and Virmani lab ID is established via secure server site
  2. Some of the data were not in SECTRA and don't have MRN (stored by name) but there exists a mapping table to ARIESID for all (we think)
  3. This lab has loaded data to ~200 ID to SECTRA since ~2-3 years ago but older scans are on CD / hard drive in the lab
    1. OSF = "OutSideFilms" - initial project MR 
      1. some have multiple timepoints (watch for longitudinal changes)
    2. CT may have been used on pt that have Deep Brain Stim equipment installed - let's leave these out for now
    3. Dr. Virmani's lab would have to tell us which strings describing which scans to share
    4. DATSCAN SPECT PET scans - should also be ignored at this time
  4. Start loading "things" to ARIES using the SECTRA PACS to pull to Posda & curate there.
    1. Phil may be getting added to this IRB to facilitate, email from Tuhin came recently discussing "routine clinical data includes images"
  5. Many dates will be converted into intervals, perhaps age-at-time-of-X
  6. There are items in AccessDB that are being converted to REDcap, how do I then put that into ARIES (from REDcap)

Collection 2: Dataset(s) from NDLAaron
  1. Passthrough ARIES IDs? Or consistent process through Sohrab's tool for this lab's project IDs? He can set this up for NDL (does not have linkages required for AR-CDR or SECTRA
  2. Discussion with Aaron and Bill to set up sharedrive to pull data into Posda
    1. ORIGINAL DATA: DICOM
    2. "Processed Data" - NIfTI then (BIDS which also works with EEG format with JSON sidecar) CIfTI?  (to consider later)
    3. Spreadsheets associated have been deidentified; do NOT yet have ARIES ID in the spreadsheets - interval offsets can be applied programmatically but may not yet have been

Collection 3: Dataset(s) from IoAAaron
  1. Sohrab needs to know who from their team needs access to the utility that will create IDs for their study
  2. Aaron can pass a bag of disks of images for import to Posda
  3. This group is not planning to provide table data that doesn't already exist in the data warehouse (so we should leave that in its native form)
  4. Which study were these subjects consented under - 

Collection 4: Dataset(s) from MMdbPhil
  1. Can pull from SECTRA to Posda with project distinctions via AETitles
  2. Quasar got Posda test up and running, Michael is downloading images and Terri can be trained when Bill are back

Collection 5: Dataset for Wardell and Rodriguez GBMPhil

(data warehouse / EPIC / images)

these data might be fit for HPCcluster - Neurodocker container would need converted to singularity; singularity works better on a shared system than docker does

get neuro pipelines set up (test to get data from PRISM into local HPC quickly)


On the HorizonFred

Brukker etc for small animal imaging

NIfTI

CIfTI

BIDS

Aperio

Action items

  • Stand up a wiki
    • meeting notes
    • collections status
    • infrastructure status (infrastructure notes page that is team-restricted)
  • Plan next step toward Neurocog data transfer: NOT YET.
  • Plan next steps toward DICOM data transfer
    • Posda instance upgrade
      • Does Posda meet EU security requirements?
    • NBIA instance upgrade
      • Tell team members ( Aaron, Jeff, tracy) what the NBIA front end address is so we can start to curate there? – NEED TO Follow up on kirk's detailed notes from the ARIES security meeting on Jun 16
      • confluence and wordpress pieces should know how they will know about each other
    • SECTRA PACS send of TT3 (nonTCIA) data
  • Next step for Gait lab data transfer

  • Aaron reports Gohar will input their subject ID / MRN and Sohrab can work with those; then we can use the ARIES ID to link to (b) SECTRA and (c) AR-CDR

  • Sohrab & Mahanaz are writing a paper about mapping identities for J Biomed Inform with Fred; this describes both “giving you a new ID” and “taking your research ID” into the database.

  • Phil and Michael have a functioning query-retrieve from the SECTRA PACS. This has fed 10 data to "TCIA test dev Posda", Bill reports he and Terri are doing well managing this process. They are preparing to set up pipelines to feed to ARIES-Posda as well.

  • What's the priority of handling non-image data - what targeted goals can we set up between Jonathan and Aaron and (others) - what targeted goals can we set up between Jonathan and Phil and the data warehouse (is ARIES designed for research datasets NOT in the DataWarehouse?)
    • Convert (what of Aaron's data) to JSON in Posda 
    • What info then goes to a triple-store; document the processes. this is the experiment for how to build things for Datascope or PRISM?
    • Aaron as a posterchild for streaming data through containers from ARIES into high performance compute for processing (e.g. dynamic fcMRI via FSL)
  • 8-23-19 Bill can send from Horos to ARIES but there's nothing at the NBIA end we can send to today
  • 8-23-19 Jeff has finished branding + structure today and tomorrow - Fred to work with him on Menu items
  • 8-23-19 Kirk has tested user access UAT and is confident we can use that
  • Stand up ARIES, clone it, ship to SBIES.
  • NICHD uses "DASH" a public database for clinical trials - by the end of January we're supposed to upload one of our own peds' clinicaltrials data to this database to make it accessible - what's their platform and how are they accomplishing it (1) put in metadata, (2) describe the schema (3) uploads PDF  (data available for download in "xpt SAS format")