Once the CLI is installed, use your API key to login to your instance of Flywheel:
Login
$ fw login my-key You are now logged in as Nathaniel Kofalt!
Try running fw without any arguments to get a feel for what commands are available.
With any command, you can add -h or --help to get more information. For example, with the download command that we will see in the next section:
Help
$ fw download -h Download a remote file or container Usage: fw download [source-path] [flags] Flags: -e, --exclude stringSlice Download everything but these types -f, --force Force download, without prompting -h, --help help for download -i, --include stringSlice Download only these types -o, --output string Destination filename (-- for stdout)
We can start with fw ls:
Viewing
$ fw ls admin neuroscience admin clinical admin psychology
This lists the groups available to you, alongside your current permission level.
Note: Site Admin users can access all groups and projects (similar to Manage Site mode in the Web UI) by adding the -a or --all flag to the CLI command.
You can ls further into the hierarchy, much as you would with your system ls command:
ls
$ fw ls neuroscience admin Amygdala Structure admin Cerebellum Circuitry $ fw ls "neuroscience/Cerebellum Circuitry" admin May 7 08:42 ccirc_sub_1 ccirc_sub_1_ccirc_ses2_protB admin Jan 7 17:30 ccirc_sub_1 ccirc_sub_1_ccirc_ses1_protA # ... admin Jun 14 16:52 InformedConsent_MRI.pdf
This shows the projects, and then sessions. For sessions, you can see the timestamp and subject code.
The last entry is an attachment on the project. You can download a file the same way you ls:
Project Session
$ fw download "neuroscience/Cerebellum Circuitry/InformedConsent_MRI.pdf" Wrote 104 kB to InformedConsent_MRI.pdf
You can also download a project, session, or acquisition:
Download
$ fw download "neuroscience/Cerebellum Circuitry" This download will be about 14 GB comprising 1865 files. Continue? (yes/no): # ...
To upload a file, enter the name of the container, and then the file path:
Upload
$ fw upload "neuroscience/Cerebellum Circuitry" config.json Uploaded file to neuroscience/Cerebellum Circuitry.
You will then see the file in your next ls:
Result
$ fw ls "neuroscience/Cerebellum Circuitry" admin May 7 08:42 ccirc_sub_1 ccirc_sub_1_ccirc_ses2_protB admin Jan 7 17:30 ccirc_sub_1 ccirc_sub_1_ccirc_ses1_protA # ... admin Jun 14 16:52 InformedConsent_MRI.pdf admin Sep 8 16:38 config.json
You can launch a job from the command-line the same way you would from the web UI.
First, have a look at what gears are available:
Jobs
$ fw job list-gears dcm2niixDCM2NIIX: dcm2nii DICOM to NIfTI converter dicom-mr-classifier SciTran: DICOM MR Classifier mriqc MRIQC: No-reference image quality metrics for quality assessment of MRI
Let's run the dcm2niix gear.
DCM2NIIX
$ fw job run dcm2niix dcm2niix_input is a required field.
This gear requires one file as its input. The full available configuration can be see by adding -h:
Input
$ fw job run dcm2niix -h Start a job. Usage: run [flags] Flags: --anonymize_bids string Anonymize BIDS (y/n, default n) --bids_sidecar string Output BIDS sidecar in JSON format. Options are 'y'=yes, 'n'=no, and 'o'=only (whereby no NIfTI file will be generated). Default='n'. --compress_nifti string Compress output NIfTI file (y/n/3, default y) [y=pigz, n=no, 3=no,3D]. Note that if option '3' is chosen, the filename flag will be set to '-f %p_%s' to prevent overwriting files --convert_only_series string only convert this series number - can be used up to 16 times (default convert all). Provide series numbers in a space-separated list e.g., '12 13' # ...
For this example, we're only going to provide the file. The path to a file is specified the same way you would ls, and set it as the flag requested earlier:
Profile File
$ fw job run dcm2niix --dcm2niix_input "clinical/Lung/anx_s2_anx_ses1_protA/fMRI high-res/468_8_1_fmri.dcm.zip"
Job configuration:
{
"anonymize_bids": "n",
"bids_sidecar": "n",
"compress_nifti": "y",
"crop": "n",
"decompress_dicoms": false,
"filename": "%f",
"ignore_derived": "n",
"merge2d": "n",
"philips_scaling": "y",
"single_file_mode": "n",
"text_notes_private": "n"
}
Job 59b2cac6ac35d80017d289c3 has been queued.
You can check on the status of your job, or wait for it to complete:
Check Status
$ fw job status 59b2cac6ac35d80017d289c3 Job 59b2cac6ac35d80017d289c3 is complete.
$ fw job wait 59b2cac6ac35d80017d289c3 Job is complete
The exit status of fw job wait will indicate if the job succeeded.