reminder for today's talk: auto QC in pediatric population
Raamana, Pradeep Reddy
a gentle reminder for today’s talk in about an hour (11am EDT) by Prof. Tonya White on automatic quality assessment of structural MRI images in children. Auto QC methods are the most sought after for obvious reasons, and the general approach generalizes across different populations, while the artefacts, specific features and models may vary. Please forward it to anyone you think might be interested.
Join via this zoom room https://pitt.zoom.us/j/3750271811
More details: https://crossinvalidation.com/2021/07/19/announcing-quality-conversations-webinar-series-on-niqc-open-science-etc/
Raamana, Pradeep Reddy
Hi everyone,
- Very glad to report the talk by Prof. Tonya White went very well! Here is the link to the video recording: https://youtu.be/8QYirk8opLA
- A clear need we identified from the discussion around auto QC is a standardized visual rating protocol to produce reliable quality ratings that ML/stats can target and optimize towards. That doesn’t exist today, and I am wondering if we can form small taskforce to define it? It’s rather straightforward (based on my research and understanding while developing visualqc for T1w mri), and I feel it’s feasible target for the first standard coming out of this SIG. Let me know if you have experience in this and/or are interested in helping develop this standard.
- Auto QC models targeting this standard can then be evaluated / validated on an open dataset or two, in a challenge-like fashion. But we need to have a standard first.
Aina Puce
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Indiana University, Bloomington IN 47405 USA
Dr Cyril, Pernet
following up on the last few weeks discussion and Yarik provocative
results :-), Patrick Fisher (who joined the google group) and myself
have decided to implement a weekly QC for fMRI for our 2 machines (a
Prisma and a PET/MR). Currently the clinical people do a standard T1/T2
to check for obvious artefacts but that's about it - so we'll pump this
up :-)
Here is our plan, but I'd like the input from the group since we will
also share those data :-) and this can be used for some work we want to do
- 1/2 hour max including set-up
- standard phantom (need to find out exactly what we have - I'm new to
the lab in Copenhagen ...) but we wouldn't buy anything new
- scan once a week but sample pseudorandomly (ie not just all Monday AM,
or all Friday PM)
- T1/T2 with the same parameters as what is typically done here for our
research protocols
- T2*EPI for BOLD; here I was thinking of 2 runs, one matching the
'standard' fmri done here and one with all gizmos on at maximum (in
plane (grappa) and in volume (sms) accelerations with the fastest TR
possible) ; how long those should be? longer better I guess, temporal
SNR variance could matter for dynamic FC? no idea
- should we do a DWI? - do we actually expect changes here not captured
otherwise
Maybe others here would want to set-up an equivalent / same QC so we
would have the 'same' data from different places
Cheers
Patrick and Cyril
--
Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
Neurobiology Research Unit,
Building 8057, Blegdamsvej 9
Copenhagen University Hospital, Rigshospitalet
DK-2100 Copenhagen, Denmark
wamc...@gmail.com
https://cpernet.github.io/
https://orcid.org/0000-0003-4010-4632
Raamana, Pradeep Reddy
Certainly – perhaps I should have elaborated, the taskforce/sub-SIG I am proposing is to draft a candidate standard (for visual quality rating for T1w MRI) that is to be reviewed by independent experts in OHBM BPC, Aperture and/or elsewhere as needed for publication and community endorsement. Some here may remember, given the large number and diversity of QC tasks, the SIG discussed early on the idea of small subgroups/task-forces focus on a well-defined QC task and build them up. Hope that makes sense.
Dr. Van Horn and I did have a long and productive conversation last month, and we’re on the same page and support each other 100%.
Peter Bandettini
Yes, we have been in discussions on this for some time. I’ve been out of the loop for a bit – taking some time off to hike in the mountains – but now mostly back.
I do think that this should be generalized to fMRI time series QC metrics reporting standard statement from BPC but one step at a time I suppose.
Best,
Peter
Aina Puce, PhD .
Eleanor Cox Riggs Professor
Psychological & Brain Sciences
Programs in Neuroscience, Cognitive Science
Affiliate, Indiana University Network Science Institute
Indiana University, Bloomington IN 47405 USA
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Chair-Past, Organization for Human Brain Mapping
Associate Editor, Perspectives on Psychological Science
--
email: aina...@indiana.edu
Twitter: @aina_puce
tel (cell): +1 812 650-2213
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