FlyWheel

FlyWheel

The Spinoza Flywheel database can be accessed with your Spinoza account through:

Introduction

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 unncessary to attach local storage such as hard drives or USB sticks to the host computer, which therefore is no longer allowed. In the following, the process from data acquisition to data access is described.

Start of a project

For new studies, a project is defined in XNAT. A user account wll be created for the primary researcher as indicated on the project form. Additional accounts can be requested from [email protected]. In addition, a project folder is created on the ftp server. From the scanners, files as well as folders can be dragged into this folder (e.g. physiology log files). The SC staff will complete the required steps to automate date export.

During and after scanning

Scans are immediately forwarded to the network after completion (i.e. reconstruction is finished). Depending on the amount of data in a scan, this will take more or less time.

Error creating thumbnail: File missing

After a session is fully processed by XNAT, you will receive an email with a link to review the content of the archived data (see example on the right).

If you do not receive an email within roughly an hour after scanning, send an email to [email protected] so SC staff can investigate the cause.

Error creating thumbnail: File missing

In addition to the email you receive from XNAT it is possible to receive additional emails detailing the export process (see example) allowing you to follow the export in more detail. This option is disabled by default.

XNAT

Paraphrasing the XNAT website, XNAT is an open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, XNAT can be used to support a wide range of imaging-based projects [1]. The Spinoza XNAT system can be found at https://ftpsc.spinozacentre.nl/xnat/.

• 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), plus the projects that have a public or protected status (by default, your project will be defined as private). See the images below for details.

• Clicking a project will show a list of MR sessions that have been stored. In addition, several tabs are available:
• Access: for controlling who can see the project and/or access data
• Manage: for setting, among other things, who should receive email from XNAT (e.g. on incoming data), and what should be done with incoming data that conflicts with existing data
• Pipelines: for enabling/disabling the automatic execution of (analysis) scripts on data, e.g. DICOM to NIFTI conversion.

• Clicking on a session will show an overview of the data stored in XNAT with details such as file size and acquisition series number. Clicking the '+' gives additional info on the acquired sequence. Hovering over the details in the "File" column will show additional data types (e.g. if images have been converted to NIFTI).

• Error creating thumbnail: File missing
  Home screen
  1. List of projects
  2. Menu for selecting project or data types
  3. View and change account info
• Project details 1. Archived scanning sessions 2. Tabs to control project access, settings, and analysis pipelines 3. Download images
  Project details
  1. Archived scanning sessions
  2. Tabs to control project access, settings, and analysis pipelines
  3. Download images
• Session details 1. Data overview 2. Foldout for more details 3. Launch pipeline 4. Download images
  Session details
  1. Data overview
  2. Foldout for more details
  3. Launch pipeline
  4. Download images
• Error creating thumbnail: File missing
  Download screen
  

Downloading data

Data can be downloaded from XNAT through two different interfaces or through a set of Matlab scripts.

Manage files

Error creating thumbnail: File missing

This interface allows you to download files (dicoms, nifti’s generated in the dcm2nii pipeline, quality assessment measures from the QAP pipeline) as a single compressed file (zip, tar or tar.gz). When this function is selected after opening a scan session, a window is opened showing all files for that session. You can easily (de)select the files of your choosing and press download.

Download images

Error creating thumbnail: File missing

The main download interface is currently Java-based, and allows for downloading of data at the project and session level. Regretfully, this interface has very limited browser support. You can use either Internet Explorer, Safari or the "Extended support release" of Firefox.

In the download window, you can

1. select which sessions should be included in the download (unless you are downloading on session level, in which case only the specific session will be available)
2. select which data formats (e.g. DICOM, NIFTI) and sequences (EPI, T1 etc.) should be exported
3. control (to a certain extent) the structure of the downloaded files by moving separate subjects into subfolders

It is also possible to download data using File:MatNat.zip, a set of Matlab scripts.

Pipelines

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

• DICOM to NIFTI conversion (based on dcm2niix)
• Quality Assessment: calculation of functional and structural imaging quality metrics (based on the PCP Quality Assessment Protocol

Pipelines can be added to a project by

• clicking the "Pipelines" tab in the project view, and subsequently
• clicking "Add more pipelines",
• choosing the desired pipeline(s) from the pipeline overview
• defining the desired settings
  • Note: make sure to choose auto launch when adding the pipeline as this setting cannot be modified later on
  • Note: please do not switch on the 'debug' option in the Pipeline Setup

• Error creating thumbnail: File missing
  Partial pipeline overview
• Error creating thumbnail: File missing
  Pipeline settings
  1. Set auto launch to yes
  2. Set desired parameters to yes
  3. Notify on completion of analysis?

QA (WIP)

You can use the QAP pipelines to calculate some basic quality metrics of your data. We are currently assessing to what extent the in vivo results obtained by running the PCP Quality Assessment Protocol provide reliable information on the scanner status.

Exporting and accessing non-DICOM data

If you collect other data, e.g. raw data or physiology, these can be exported to the network drive mounted on the scanners. Projects are located in S:\projects. Note that while you cannot enter your project folder (for privacy reasons), you can drag and drop files and folders into them and subsequently access them via FTP.

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:\

SFTP

• The ftp server address is sftp://ftpsc.spinozacentre.nl/.
• We recommend using FileZilla as client to connect to the FTP server.
• You can log in with the credentials you received upon starting your project.

Naming conventions

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
SC-develop_3D-EPICS_test
etc.

To export, examcards also need to have autopush enabled, and pushnode flywheel set to 'yes'.

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 

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.

Please add the name of the MR operator in the "Performing Physician" field.
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.

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. In order for the conversion to go smoothly, FlyWheel encourages the use of the ReproIn naming scheme, outlined on this website.

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 sequences (optional)

Functional 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 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

Importing non-dicom data

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 adn subject naming convention outlined above, FlyWheel will create automatically create an import folder on the 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.

FlyWheel support options

• You can email directly to [email protected]. And one of our support engineers will get back to you.
• You can go to Flywheel webpage https://flywheel.io/

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:

• Quick Start Guide
• How to Find your data on Flywheel
• User, Roles and Permissions on Flywheel
• Data import
• recorded Flywheel webinars