Flywheel Tutorial

Date: February 24, 2025 3:56 PM

FLYWHEEL LINK: https://cahbir-flywheel.rutgers.edu/#/projects

Table of Contents

Flywheel Tutorial

High level process

Download data to amarel
Multi-echo multi-band Convert using Jeff custom method
- reproIn
- this assigns echo1 echo2 echo3 to the bids name
- then it does the dcm2niix
Then the MRI Tech uploads the data to flywheel
Then you send to BIDS Curation
then you send to fMRIPrep
Then download subject to box OR open flywheel on Amarel desktop and download to amarel, or use custom python script to download to Amarel
Then share

How to change file names (if necessary):

Tutorial by flywheel devs: https://docs.flywheel.io/Developer_Guides/dev_bids_curation_2_precuration/

Go to your Project tab
click on Subjects tab and select the subject you’d like to run
Go to Analysis tab
Click Run analysis gear
Click “Bids Pre-Curation” or “relabel container” (they’re equivalent)
1. put in no inputs, leave everything blank
run gear
Go to subjects tab
to go “provenance” tab in subject to see the job running
1. refresh for new update— not live view
2. if fails, click on the “View Log” button
3. read the error log to figure out
  1. ask Wil if need be
When finished, go to “analysis” tab at the TOP (not within “Subject”)
click on the job Bids pre-curate
For the files, if you need to make edits, press on the 3 dots and then press “Download”
acquisitions.csv
sessions.csv
subjects.csv
make the edits in excel
in flywheel, in the project tab, press “information” tab
press ‘upload’
upload the .csv that you made edits to
- This keeps the version history of all the prior csv versions— so if you upload a document that is wrong, you can just restore an old version

Ignoring Files

If you need to ignore 1-3 images into .bidsignore…

Flywheel Tutorial: Ignoring Certain Images in Bids

Go to your Project tab
click on Subjects tab and select the subject you’d like to run
go to Sessions tab
make sure you’re on “Acquisitions” tab
optional: Turn on “BIDS View”
1. click on the 3 dots to the right of the “Run Gear’ button
2. click on the on-switch for “BIDS View”
click on the file you want to ignore
in the popup, go to “Information” tab
scroll down to the small section which says “BIDS” and has a carrot “^”
Press on the carrot to expant the BIDS information
Scroll down to the line “ignore []” and check the box
Press “save” on the popup
Repeat steps 6-11 for any files you want to ignore

If you need to ignore many images based on rules…

click on your project tab
Go to “Information”
In files find template nordic_extension_template.json If it’s not already uploaded, upload into the project files nordic_extension_template.json, by clicking on: - Project Name (in side navigation bar) - Information tab - Attachments box - ‘Upload’ button
Click on the 3 dots in the template row and click “Download”
Open file in an editor
in the “initializers:” section, paste in your code

for example, this skips any files which start with “fmap_” or “fmap-” and end with “SBRef” or “Pha”, and skips any files which end with “_e2” or “_e3”

{
          "rule": "reproin_fieldmap_file",
          "where": {
            "acquisition.label": {
              "$regex": "fmap(-|_).*(SBRef|Pha)+$"
            }
          },
          "initialize": {
            "ignore": true
          }
        },
        {
            "rule": "reproin_fieldmap_file",
            "where": {
                "file.name": {
                    "$regex": "_e(2|3)\\.(nii(\\.gz|)|json)$"
                },
                "acquisition.label": {
                    "$regex": "fmap(-|_)"
                }
            },
            "initialize": {
                "Suffix": "echo",
                "ignore": true
            }
        },

Download Files

The command line is where you can download BIDS files to Amarel/local computers, as well as download individual subjects or acquisitions quickly.

See how to set up and use it on the Flywheel CLI Tutorial.

Add Files to Projects/Sessions/Subjects

Flywheel allows ‘ad-hoc’ upload, so you can add any type of file to a dataset.

For project-level (templates, etc): Click on: - Project Name (in side navigation bar) - Information tab - Attachments box - ‘Upload’ button

For acquisition or subject files: Click on: - Project Name (in side navigation bar) - ‘…’ vertical dot menu - ‘Imports’ - ‘Add Data’

Flywheel Storage & Pipeline Rules

No restrictions for the amount of data
But we’re charged for the data since it’s stored in google cloud
In general it won’t cause a problem
Can keep all your scanning data on flywheel
- More likely to stay stable than stuff you take off and put on amarel
After every session of fMRI scanning at CAHBIR the scan tech is going to automatically send data from the scanner to flywheel
- multi-band multi-echo will go up but will go up a little later since Jeff has to do another step
- compress-sensing MP2Rage
Double check that the information you want in flywheel is being transferred after the data is put into flywheel
- You should definitely do a test or two with your pipeline

BIDS process

click on the project you want to look at (ie ConteCenter, PCX)
click on ”Sessions” tab
Make sure you’re on “Acquisitions” tab
Click ‘Run Gear’
Select ‘Analysis Gear’
Select ‘BIDS Curation’
Click on the project name
‘Inputs’ tab:
1. click on “template”
2. click on ConteCenter or your project name (in the folder path)
3. select the nordic_extension_template.json
  - locates and assigns the echoes their proper echo name
  - ignores single band reference images and phase images for fieldmaps
  - If it’s not already there, upload it to the project files by clicking on:
  - Project Name (in side navigation bar)
  - Information tab
  - Attachments box
  - ‘Upload’ button
‘Configuration’ tab:
1. First: you need to specify the regexes in pairs, each element separated by a space.
  1. To attach all fmap to their relevant BOLD images: fmap-.* .*bold.nii.gz You have to match the fmap container to the functional images containers. Our containers for Conte/PCX are (both AP and PA):
    - fmap-epi_dir-AP_BOLD_NORDIC_run-01
    - fmap-fieldmap_acq-B0
    - fmap-phasediff_dir-AP
    Our functional images are
    - func-epi_task-_BOLD_NORDIC_run-01
    So to map (fill intendedFor field) every fmap to the functional images, use fmap-.* .*bold.nii.gz EX: To just map epi fmaps to the functional images, use fmap-epi_.* .*bold.nii.gz
2. Reset: YES
3. Ignore Config File: YES
4. Save idecar as Metadata: NO
  - the JSON sidecars of the data to fill in the configuration, but you can add additional stuff in the tab that isn’t in the sidecars
Go to jobs log tab to track usage or errors
1. Select subject/job
2. Select ‘log’ tab
  - Refresh to see current— not in real time

Getting BIDS to work on Flywheel

fMRIPrep process

‘Run gear’
‘run analysis gear’
- NOT ‘fMRIPREP: A robust…”
- Select “BIDS Apps: BIDS fMRIPrep” to run
Input
- Add in your FreeSurfer license file freesurfer_license_jun2024.txt
  - way1: copy contents of text file > configuration > ‘gear FREESURFER LICENSE’
  - way2: Information > Attachments > Attach freesurfer license .txt
  - way3: Information > Custom Information > ‘+’ called FREESURFER_LICENSE > copy paste the .txt file into there
    # my freesurfer license: josskaley@gmail.com 76240 *CV/FoHsRCHG2 FSog2TzUed5Oc /acN2e0Wjauej8YOxxyyIFs1Jqd30/Kl3WV41M3fnfQ=
Job Tags: ‘extra-large’
Configuration -
- most recent is 1.5.1_24.0.0, but can choose your version
- bids_app_command for PCR:
`fmriprep bids_dir output --no-submm-recon --bold2anat-dof 6 --output-spaces T1w fsnative fsaverage MNI152NLin2009cAsym:res-native MNI152NLin2009cAsym:res-2 --cifti-output 91k --write-graph`
Finally, press ‘Run Gear’
Wait 12-24 hours

Getting fMRIPrep to work on Flywheel

Misc

Command Line

set up a command line interface
initials > profile > flywheel CLI Classic > download Classic CLI > setup API key (copy it while it’s there, it will never be visible again) > use command line to export your project in bids format
- you can do this on amarel and export directly to amarel

Add Additional Documents

‘ad-hoc’ upload
can add any type of file to a dataset

Flywheel Storage & Pipeline - only put active CAHBIR center data

no restrictions for the amount of data
but we’re charged for the data since it’s stored in google cloud
but in general it won’t cause a problem
Can keep all your data on flywheel
- more likely to stay stable than stuff you take off and put on amarel
After every session of fMRI scanning at CAHBIR the scan tech is going to automatically send data from the scanner to flywheel
- multi-band multi-echo will go up but will go up a little later since Jeff has to do another step
- compress-sensing MP2Rage
Double check that the information you want in flywheel is being transferred after the data is put into flywheel
- You should definitely do a test or two with your pipeline

Data-Viewer

little picture icon on the right of the dicom
can also double check that your files are right

Gear Exchange

flywheel.io/gear-exchange/
- if there’s any there you want and aren’t currently installed on our flywheel, let Wil / CAHBIR-support know, and they’ll ask flywheel to add it
You can also make requests for flywheel to make a gear, though we don’t know how quickly that might happen

Other

Wil custom python script
- will unzip and grab specific files and put them where you want them to be

Questions

Flywheel has robust documentation
- https://docs.flywheel.io/Developer_Guides
or email flywheel directly with ‘give us feedback’ (opens up a ticket)

Data-Viewer

little picture icon on the right of the dicom
can also double check that your files are right

Gear Exchange

flywheel.io/gear-exchange/
- if there’s any there you want and aren’t currently installed on our flywheel, let Wil / CAHBIR-support know, and they’ll ask flywheel to add it
You can also make requests for flywheel to make a gear, though we don’t know how quickly that might happen

Other

Wil custom python script
- will unzip and grab specific files and put them where you want them to be
Questions
- Flywheel has robust documentation
- or email flywheel directly with ‘give us feedback’ (opens up a ticket)