FlyWheel: Difference between revisions
From SpinozaWiki
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Cerebellum_sub001_ses001 | Cerebellum_sub001_ses001 | ||
etc. | etc. | ||
<br> | |||
Do '''not''' use | |||
Do not use | |||
<projectID>_<subjectID> | <projectID>_<subjectID> | ||
as this will lead to the subject being named projectID and the session 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 <br> | |||
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. <br> | 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. <br> | ||
Revision as of 13:18, 26 October 2021
FlyWheel
Database
The Spinoza Flywheel database can be accessed with your Spinoza account through: https://spinozacentre.flywheel.io/
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.
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: