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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 it would be just 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 convention described in the ReproIn section. If any metadata (subject_id or session_id) need to be corrected, inform 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 fashion way

scp or rsync. But you would need to take care about 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 folders with original DICOMS and possible derivatives (fmriqc, etc).