[meeting] Phantom QA/QC
Raamana, Pradeep Reddy
Thanks everyone for replying to doodle poll – it appears the best time for Phantom QA/QC meeting would be Tuesday July 27th 2-4pm EST. I would like a volunteer or two to give a short informal talk on the rough landscape related to Phantom QA/QC just to set the stage for an open discussion on challenges and potential solutions etc – let me know.
Also, thanks to those who suggested some topics and speakers already via this form https://forms.gle/Ggkw89UKwGv7bkxD9 - please feel free to suggest more. Someone suggested me to discuss an important topic, but I need few more details on get a better idea on this suggestion, and hence I request them to kindly make another suggestion with more details (or email me directly, not reply all).
FYI consider this to be the first event in the Quality Conversations webinar series that I am very delighted to announce, and I am really excited about future talks here. There is a google calendar link there that can subscribe to, which will also have all niQC events:
Thanks,
Pradeep
Raamana, Pradeep Reddy
My bad, the timing is 4-6pm EST (not 2-4pm) on Tuesday July 27th. Thanks Yarik for catching the mistake.
Peter Bandettini
Hi Pradeep,
I’ll be out of town until Aug 5, but if there’s any chance you could record this, I would be very interested in seeing it the moment I get back from holiday.
Best,
Peter
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Raamana, Pradeep Reddy
Certainly – we plan to record all the meetings and share them as soon as possible.
We will be collecting the notes from that meeting in this google doc – please feel free to add/edit:
https://docs.google.com/document/d/1ErjJpkf24btmjUOk6uEs9FpvdQARPPpBllk23KB85-Q/edit?usp=sharing
Stephen Strother
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JB Poline
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Raamana, Pradeep Reddy
No problem Stephen and JB. Looking forward to seeing those who can make it tomorrow (reminder its from 4-6 PM EST). Everyone, please feel free to share any phantom QA/QC papers in neuroimaging we must all read or atleast be aware of?
Thanks,
Pradeep
From: JB Poline <jbpo...@gmail.com>
Date: Sunday, July 25, 2021 at 1:40 PM
To: Raamana, Pradeep Reddy <RAAM...@pitt.edu>
JB Poline
Raamana, Pradeep Reddy
Yes, It does exist, forgot to mention: https://www.zotero.org/groups/2221093/niqc
Todd Constable
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Raamana, Pradeep Reddy
Thank you Todd, glad to hear that. This collection is necessarily incomplete, and I would appreciate everyone adding relevant papers as they come across them. I just added a few more on phantoms, fMRI QA, and DWI QA as I was preparing for the phantom meeting today.
Reminder everyone, it is in a few hours (4-6pm EST) at https://pitt.zoom.us/j/3750271811
Few thoughts:
- It is not clear if the fBIRN recommendations (fMRI QA) are complete! I would like to learn where the gray areas or newly identified challenges exist (e.g. since 2015).
- Given the adoption of fBIRN recommendations in many large multi-center neuroimaging studies, are they ready to be termed THE best practices (“beatified”)? If not, where do we need more evidence or consensus?
- QA for DWI and fMRI are different beasts, and we may need somewhat separate streams of discussions
Thanks,
Pradeep
Raamana, Pradeep Reddy
I am glad to report the open/panel discussion on the role of phantoms in neuroimaging QA/QC went very well.
Rough notes and video link are below. We have a few exciting talks coming up, the next one by Prof. Tonya White on Aug 12th 11am EDT on automatic quality assessment in pediatric imaging data. Please join us and suggest other speakers/topics here, including nominating yourself.
Notes from Phantom QA/QC discussion on July 27, 2021:
- Here is the video https://youtu.be/HcS9_LFdoPw
- Yarik’s talk:
- His interest in phantoms
- Reproducibility crisis
- Improving SNR besides improving sample sizes
- They are cheap, known stable characteristics, easy to build,
- If scanner is working okay, people usually discard phantom data
- As they are not considered useful beyond QA
- Slice-wise artefacts exist, that can go unnoticed for years
- fBIRN protocol is not always followed?
- Phantom data is almost never shared
- Action items
- Tools to extract all relevant info from DICOMS into Nifit/BIDS
- For sharing
- Perhaps we might need a BIDS extension for Phantom data?
- Possibilities for inclusion of phantom into the current spec:
- Tags in subject JSON to link to the relevant phantom?
- Cross-links between phantoms and subjects
- adapted pybids / validation for phantom-related data?
- DICOM is the preferred format for phantoms to capture more info and meta-data
- NITRC is a good repository for sharing phantom datasets, as it can accept and handle DICOMS, whereas other platforms may not
- A great incentive we can offer scientists to share phantoms is to show that it increases the statistical power of their datasets (to be proven)
- A concern for PIs in sharing phantom data is the risk of potential identification of issues in their datasets or analyses or papers.
- We need to address it (more education) and find ways to mitigate it (anonymizing the dataset in terms of specific study or PI?)
- Challenges in using phantom data for analyses
- Date/phantom/subject matching
- Possible solutions:
- Matching based on meta data
- Matching based on noise patterns outside the brain
- Need a new QA metric: multi-band slice leakage metric (spillage etc)
- Needs to be validated
- There may be a need to update/revise the fBIRN QA recommendations
- Alex Franco:
- time of day effects exists in SNR
- Cyril Pernet:
- Resolution for phantom and T1w images are not the same thermal noise is not the same
- New datasets
- Lei Wang
- Starting a new multi-site study. Will be sharing a phantom dataset, to be acquired with ABCD protocol from 7 sites
- Help looking for: methods and software to quantify quality and reveal any issues
- Erin Dickie / CAMH
- Is looking into sharing a dataset
- Jo Etzel / WASHU
- Is working on sharing a dataset
- Existing: datasets from OBI Canada already linked in niQC website
- A new white paper summarizing the above would be the way to go
- Yarik may take the lead
Aina Puce
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Indiana University, Bloomington IN 47405 USA
Yaroslav Halchenko
Raamana, Pradeep Reddy
Thanks Yarik – I’ve started adding my comments to this white paper draft. I just came across this nice review on QA this week and added it to the niQC Zotero collection with few others:
Lu, W., Dong, K., Cui, D., Jiao, Q., & Qiu, J. (2019). Quality assurance of human functional magnetic resonance imaging: A literature review. Quantitative Imaging in Medicine and Surgery, 9(6), 1147–1162. https://doi.org/10.21037/qims.2019.04.18
Everyone, I’m glad to report both the Gold Standard Phantoms and Phantom Lab companies agreed to present their services and perspectives, and we’re trying to find a good time. The QC webinar series schedule has slots in the 4th week of August – would that work for everyone? I don’t want to run a doodle poll, but I don’t want to clash it with any other conference/workshop that might take those interested away from it either. Let me know (not reply all) with your preferences.
If we missed any other good companies/products that we must hear from, let me know.
- Resolution for phantom and T1w images are not the same à thermal noise is not the same
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Aina Puce
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