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Neuroimaging Data Access

All data is collected and provided for access and conversion into BIDS on rolando.cns.dartmouth.edu.

You need to request access permissions from Research Computing.

---
config:
      theme: redux
---
flowchart TD

subgraph subGraph1["Source Data from Scanner"]
       inbox-dicom(("/inbox/DICOM"))
       details1("Accessions stored by date<br>/YYYY/MM/DD/A#")
 end
subgraph subGraph2["Converted Data"]
       inbox-bids(("/inbox/BIDS"))
       details2("Stored as /PI/Lead/Study<br/><a href='https://github.com/bids-standard/bids-specification/pull/1861#issuecomment-2183701293'>BIDS Project</a><br/>under 'sourcedata/raw/'")
 end
   local-storage("local storage")
   inbox-dicom -- "<a href='https://dbic-handbook.readthedocs.io/en/latest/mri/dataaccess.html#dicoms'>scp/rsync</a>" --> local-storage
   inbox-bids -- "<a href='https://dbic-handbook.readthedocs.io/en/latest/mri/dataaccess.html#bids'>scp/rsync/DataLad</a>" --> local-storage
   inbox-dicom --> request("PI requests<br/>dataset conversion")
   request --> conversion{"<a href='https://github.com/repronim/reproin'>Reproin<br/>conversion</a>"}
   conversion --> inbox-bids


   style subGraph1 fill:#FFFFFF,stroke:#000000
   style subGraph2 fill:#FFFFFF,stroke:#000000
   style inbox-dicom fill:#C8E6C9,stroke-width:4px,stroke-dasharray: 0,stroke:#00C853
   style details1 stroke:#000000
   style inbox-bids fill:#C8E6C9,stroke-width:4px,stroke-dasharray: 0,stroke:#00C853
   style details2 stroke:#000000
   style request stroke-width:4px,stroke-dasharray: 0,fill:#FFE0B2,stroke:#00C853
   style local-storage fill:#C8E6C9,stroke-width:4px,stroke-dasharray: 0,stroke:#00C853
   style conversion stroke:#00C853,stroke-width:4px,stroke-dasharray: 0

N.B. Storing under sourcedata/raw/ is a planned solution. At the moment the data is placed in the root of the dataset.

DICOMs

All DICOMs are organized into YEAR/MONTH/DATE/ACCESSION hierarchy under /inbox/DICOM. You can scp or rsync them to your local storage.

BIDS

At the moment, upon request from a lab member to Yaroslav Halchenko, data is converted from DICOMs into BIDS within the directories hierarchy under /inbox/BIDS, following the convention described in the ReproIn section. If any metadata (subject_id or session_id) needs to be corrected, let us know ahead of time.

These directories are also DataLad datasets, so you have two options on how to transfer them:

DataLad

Before you proceed, please refer to the DataLad section of the handbook. When you are all set, you can do simply something like

datalad clone myrolandoid@rolando.cns.dartmouth.edu:/inbox/BIDS/dbic/dbic-animals dbic-animals

This will create a local clone of the dataset, and you can use datalad get to get the data you need.

Old-fashioned way

scp or rsync, but you would need to take care of de-referencing symlinks:

rsync --exclude=.git --copy-links -r \
    rolando.cns.dartmouth.edu:/inbox/BIDS/dbic/dbic-animals dbic-animals

You could add --exclude=sourcedata and/or --exclude=derivatives to exclude the folders with the original DICOMs and possible derivatives (mriqc, etc.).