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FlyWheel

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Revision as of 16:31, 17 June 2022 by Zwaag (talk | contribs) (→Naming convention for subjects)

About FlyWheel

Imaging data acquired on the MRI scanners at the Spinoza Centre are automatically transferred to FlyWheel in the DICOM format. The data can subsequently be accessed (from within and outside the Centre) in FlyWheel Within [FlyWheel], data can be converted to Nifti, and analysis pipelines can automatically run on the data. Other (imaging) data can be dropped in the subject folder that is automatically created on the "export to FlyWheel" mount on the scanner console. These options make it unnecessary to attach local storage such as hard drives or USB sticks to the host computer, which therefore is no longer allowed. In the following paragraph, the process from data acquisition to data access is described.

Paraphrasing the FlyWheel website, FlyWheel is a Biomedical Research Data Platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, FlyWheel can be used to support a wide range of imaging-based projects. The Spinoza FlyWheel platform can be accessed at FlyWheel


To re-watch the flywheel presentation we gave at Spinoza's SUM meeting, see this YouTube video


For more information about FlyWheel, you can browse through their YouTube channel.

Access

The Spinoza Flywheel database can be accessed with your Spinoza account.

  • Upon login, you will see the home screen where you will see an overview of the projects you are involved with, either as a member or owner. Please see the images below for details.

Pipelines

Several automated operations/analyses can be performed on the data when they are stored in FlyWheel. The most important ones currently in place are

  • DICOM to NIFTI conversion: dcm2niix
  • Conversion to BIDS format
  • Quality Assessment: MRIQC
  • Preprocessing: fMRIPREP


Start of a project

For new studies, a project is defined in FlyWheel by the Spinoza staff. A user account will be created for the primary researcher as indicated on the project form. Additional accounts can be requested from [email protected].

Excluding data

If you do not want your data to be sent to FlyWheel for privacy reasons or otherwise (e.g., clinical data), please add "NO" in the "Study Comments" field.

During and after scanning

Scans are added to the FlyWheel dicom transfer queue after completion, i.e. when reconstruction is finished. Depending on the amount of data in a scan, this will take more or less time.
Important: For Flywheel's automatic data import to function, examcards also need to have autopush enabled, and pushnode flywheel set to 'yes'.

Old-School: Exporting and accessing non-DICOM data

If you want to follow your old workflow for any reason, you can still output PAR/REC data from the scanner. This may be a good idea if you already have acquired data for a given subject that was exported as PAR/REC and you'd like to average the new data with the old without converting to % signal change. FlyWheel offers the option of importing PAR/REC, SPAR/SDAT and RAW MR data into their database. Also, other data such as behavioral or physiological data can easily be added to a session. If one adheres to the exam card and subject naming convention outlined below, FlyWheel will automatically create a session-specific directory is created in your project's "Group_Project" folder on the export to FlyWheel server drive (Z disk) on the console.
The import folder will be created after the first dicom series has successfully been sent from the console at the path below; 

Z:\FlyWheel\<groupID>_<projectID>\<subjectID>_<sessionID>

If you do not see this folder, this can have various causes: - The group or project does not exist in FlyWheel yet. Ask the Spinoza staff to create it for you. - There are still other send jobs in the queue before yours. You can rush the push of your scout to expedite folder creation. - Autopush is disabled in your exam card. Right-click and enable it. Make sure to save the exam card afterwards.

Manual Flywheel Import folder on the server

Automated Flywheel data import & BIDS-conversion

Flywheel can fully automatically import DICOM data from the scanner, and convert these DICOM data to nifti files. Moreover, it can automatically convert your data's filenames, metadata, and directory structure to the industry-standard BIDS naming convention. In order for the conversion to go smoothly, FlyWheel encourages the use of the ReproIn naming scheme, outlined on this website.

On the FlyWheel support website you can find a full treatment of how Flywheel imports data, and how these data are then converted to nifti, and subsequently, BIDS. Here, we're summarising these guidelines, but the original (and most recent version) can be found at run naming guidelines xls file.

Naming convention for exam cards

To enable correct dicom routing to the correct project folder and set group ownership, exam card names should adhere to the following convention:

<researchgroup>_<project>_<extra info if need be>

E.g.;

Dumoulin_SDVICI
Zwaag_Cerebellum
SC-develop_VASO
etc.


How to name an exam card

Naming convention for subjects

To enable correct dicom naming, subject IDs should adhere to one these four formats:

<subjectID>
<subjectID>_<sessionID>
<projectID>_<subjectID>_<sessionID>

E.g.;

sub001
sub001_ses001
Cerebellum_sub001_ses001
etc.

Do not use:

<projectID>_<subjectID>

as this will lead to the subject being named projectID and the session subjectID. E.g.

Cerebellum_sub001 results in the subjectID Cerebellum with sessionID sub001

Also, make sure that you use a new subjectID / sessionID for each subject in the project, or Flywheel will not send the data to your project at all, and dump it in 'unsorted'. If this happens, contact an admin (TK, WZ) to retrieve your data.

As a general rule, FlyWheel will ignore any part before the first underscore if it finds two underscores. If it finds one, it will assume the part before the underscore is the subjectID and the part after the sessionID.

Other data

If you collect other data, e.g. raw data or physiology, these can be exported to the Export to FlyWheel network drive mounted on the scanners, see above.

Some notes on exporting data to local drives:

  • Data stored on E:\Export, G:\Temp etc. should be removed after the files are copied to the project folder.
  • Data stored in these locations will be removed by SC staff without prior notice and is not backed up.
  • Never save data to C:\ or D:\

Naming convention for sequences (optional)

Functional MRI with topup

func-bold_task-<taskname>_run-01 This is run 01 of the task
fmap-epi_acq-<taskname>_run-01 This is the topup sequence that goes with run 01
func-bold_task-<taskname>_run-02 This is run 02 of the task
fmap-epi_acq-<taskname>_run-02 This is the topup sequence that goes with run 02

Functional MRI with B0

func-bold_task-<taskname>_run-03 This is run 03 of the task
fmap-B0_acq-<taskname>_run-03 This is the B0 sequence that goes with run 03

Standard Anatomy

run-01_anat-T1w This is the first T1 weighted anatomical
run-02_anat-T1w This is the second T1 weighted anatomical
anat-T2w This is the only T2 weighted anatomical
anat-T2starw This is the only T2* weighted anatomical

Fancy anatomy -- tentative (BIDS specification has changed and ReproIn is unclear)

anat-T1map_acq-MEMP2RAGE This is the only T1 map
anat-T2*map_acq-MEMP2RAGE This is the only T2* map
anat-MEMP2RAGE_[_echo-<index>]inv-1_part-mag This is the magnitude map of the first inversion in an MP2RAGE
anat-MEMP2RAGE_[_echo-<index>]inv-1_part-phase This is the phase map of the first inversion in an MP2RAGE
anat-MEMP2RAGE_[_echo-<index>]inv-2_part-mag This is the magnitude map of the second inversion in an MP2RAGE
anat-MEMP2RAGE_[_echo-<index>]inv-2_part-phase This is the phase map of the second inversion in an MP2RAGE

FlyWheel support options

Click on Support
Click on Contact support on top right corner of the page.
Fill the form with description of issue and submit. This will create a ticket and one of our support engineers will reach out to you.
  • Above form can also be accessed directly from Flywheel UI .
In Flywheel UI go to Profile page (which is on the upper right side corner of UI window).
There is a section on Flywheel resources. (See  Screen Shot 2019-12-02 at 2.45.34 PM.png) 
Click on Contact Flywheel

FlyWheel recources

Here are some links to some quick start guides, additional information on permissions and account setup and recorded webinars:

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