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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 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
  4. Start loading "things" to ARIES using the SECTRA PACS to pull to Posda & curate there.
  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

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

Collection 4: Dataset(s) from MMdbPhil
  1. Can pull from SECTRA to Posda with project distinctions via AETitles

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
    •  NBIA instance upgrade
    •  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 writng 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.

  •  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.