bidskit

Flywheel Export Support

Flywheel allows export of DICOM data from a project, subject or session from the web interface.
The most common download format is as a ZIP archive with the following internal structure:

flywheel or scitran
└── odoherty
    └── OLEL
        └── JOD_OLEL_031
            └── 1
                ├── anat-MEGRE
                │   └── 1.3.12.2.1107.5.2.43.167050.2023010410414566046477344.0.0.0.dicom.zip
                ├── anat-MEGRE RMS
                │   └── 1.3.12.2.1107.5.2.43.167050.2023010410483321035277560.0.0.0.dicom.zip
                ├── anat-MEGRE RMS_1
                │   └── 1.3.12.2.1107.5.2.43.167050.2023010410483321090177563.0.0.0.dicom.zip
                ├── anat-MEGRE_1
                │   └── 1.3.12.2.1107.5.2.43.167050.2023010410483317378977552.0.0.0.dicom.zip
                ├── anat-gre_acq-localizer
                │   └── 1.3.12.2.1107.5.2.43.167050.2023010409440829026077292.0.0.0.dicom.zip
                ├── fmap-epi_acq-olel_dir-AP_run-1
                │   └── fmap-epi_acq-olel_dir-AP_run-1.dcm
                ├── fmap-epi_acq-olel_dir-PA_run-1
                │   └── fmap-epi_acq-olel_dir-PA_run-1.dcm
                ├── func-bold_task-olel_run-1
                │   └── 1.3.12.2.1107.5.2.43.167050.202301040948137858777630.0.0.0.dicom.zip
                ├── func-bold_task-olel_run-1_PhysioLog
                │   └── func-bold_task-olel_run-1_PhysioLog.dcm
                └── func-bold_task-olel_run-1_SBRef
                    └── func-bold_task-olel_run-1_SBRef.dcm

Single DICOM series are uncompressed, but series containing more than one DICOM image file are ZIP compressed.

BIDSKIT curation of Flywheel DICOM zip archives

Create a BIDS dataset directory and move or copy all Flywheel DICOM zip archives to this directory
Run bidskit from this directory with the –flywheel command line option to unpack the tarballs into the sourcedata folder and build the template BIDS files and folders (Phase 1)
```
$ bidskit --flywheel <other command line arguments>
```
Edit code/Protocol_Translator.json manually or use the --auto option to autofill the translator file
Run bidskit again (Phase 2) without the --flywheel option to complete the curation
```
$ bidskit <other command line arguments>
```
Delete or move the original Flywheel zip archives

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