[meeting] Phantom QA/QC

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Raamana, Pradeep Reddy

Jul 19, 2021, 11:02:36 AMJul 19
to niQC

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:







Raamana, Pradeep Reddy

Jul 19, 2021, 11:35:02 AMJul 19
to niQC

My bad, the timing is 4-6pm EST (not 2-4pm) on Tuesday July 27th. Thanks Yarik for catching the mistake.

Peter Bandettini

Jul 19, 2021, 11:40:57 AMJul 19
to Raamana, Pradeep Reddy, niQC

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.





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Raamana, Pradeep Reddy

Jul 19, 2021, 12:05:02 PMJul 19
to Peter Bandettini, niQC

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:


Stephen Strother

Jul 23, 2021, 9:27:22 PMJul 23
to ni...@googlegroups.com
Will this be recorded and made available for subsequent viewing. Unfortunately I cannot tune in at those times. Regradless great to see this starting and hope it is enlightening to all.

Thanks, Stephen
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Stephen Strother, PhD
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JB Poline

Jul 25, 2021, 1:40:36 PMJul 25
to Raamana, Pradeep Reddy, NIQC, Stephen Strother
Hi Pradeep

Sorry that I cannot make it either (teaching) but would be happy to keep in touch


Raamana, Pradeep Reddy

Jul 26, 2021, 7:33:07 AMJul 26
to jbpo...@gmail.com, NIQC, Stephen Strother

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?





From: JB Poline <jbpo...@gmail.com>

Date: Sunday, July 25, 2021 at 1:40 PM
To: Raamana, Pradeep Reddy <RAAM...@pitt.edu>

JB Poline

Jul 26, 2021, 7:59:24 AMJul 26
to Raamana, Pradeep Reddy, NIQC, Stephen Strother
A zotero collection maybe ?

Raamana, Pradeep Reddy

Jul 26, 2021, 8:00:44 AMJul 26
to jbpo...@gmail.com, NIQC, Stephen Strother

Yes, It does exist, forgot to mention: https://www.zotero.org/groups/2221093/niqc

Todd Constable

Jul 26, 2021, 8:37:05 AMJul 26
to Raamana, Pradeep Reddy, Todd Constable, jbpo...@gmail.com, NIQC, Stephen Strother
Thanks for this list Pradeep - this is great!

R. Todd Constable, Ph.D.
Professor of Radiology and Biomedical Imaging, BME, Neurosurgery
Director MRI Research
Yale University School of Medicine
The Anlyan Center
300 Cedar Street
PO Box 208043
New Haven, CT 06520-8043
Website: http://mri.med.yale.edu

Raamana, Pradeep Reddy

Jul 27, 2021, 2:12:31 PMJul 27
to Todd Constable, Todd Constable, jbpo...@gmail.com, NIQC, Stephen Strother

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




Raamana, Pradeep Reddy

Jul 29, 2021, 9:32:42 AMJul 29
to niQC

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

Jul 29, 2021, 10:09:47 AMJul 29
to Raamana, Pradeep Reddy, niQC
I am looking forward to Tonya's presentation - now that we are partly open here at the university I might book the conference room & stream it in there for people - it will be nice to be together & discuss it - although we will probably wear masks...

Aina Puce, PhD . 

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Eleanor Cox Riggs Professor
Psychological & Brain Sciences
Programs in Neuroscience, Cognitive Science
Affiliate, Indiana University Network Science Institute
Indiana University, Bloomington IN 47405 USA
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

Yaroslav Halchenko

Jul 30, 2021, 8:15:32 AMJul 30
to niQC
To get ball rolling, at least at minuscule scale for starters, initiated niQC google drive folder 
https://drive.google.com/drive/folders/1GLARthHrkeTI-uKR1Iag8ZIHopUZxiJ5?usp=sharing (I guess you would need to request access which I will grant) with a whitepaper-2021 folder in it and a google doc there where I am planing to start dumping information to formalize into a paper.

Raamana, Pradeep Reddy

Aug 5, 2021, 9:56:44 AMAug 5
to Yaroslav Halchenko, niQC

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

Aina Puce

Aug 5, 2021, 10:44:37 AMAug 5
to Yaroslav Halchenko, niQC
Good idea Yarik! Then things can gradually take shape. Aina

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