[Neurobureau-hubs] Re: [rs-fMRI QC protocol]

Tue Aug 27 10:44:22 PDT 2013

Dear all,

Cameron, Alex, Donald, it's great that you are in, thanks for the
enthusiastic response.

@Donald

Le mardi 27 août 2013, MCLAREN, Donald a écrit :

> I think this is a GREAT idea. Two things that are important to consider:
> (1) pipeline independent QC metrics -- if someone is using another
> pipeline, the QC metrics should still be applicable at least for the
> pre-processing steps (e.g. motion, normalization, etc.)
>

Absolutely.

>
> (2) scanner/coil independent QC metrics -- I've seen some recent scanners
> form high channel coils that don't have uniform intensities in the raw
> images, this may or may not present a problem for standardizing QC metrics.
> Either way, it should be a consideration.
>
>
It is a problem. Some group QC we have used measure spatial correlation
of, say, average bold volume with a reference in stereotactic space.  If
there is a huge bias field, that qc metric essentially picks on the field.
NIAK has corrections built in for this though.

We could potentially test the reliability at brainhack if you think we have
> enough lead time to pilot some QC metrics. It should take too long for
> everyone to QC 10-15 brains and you would get a good sample size. We could
> reserve some time for training.
>

Totally. I'll get back to you with more detailed plans after I talk with
yassine.

Best,

Pierre

> Best Regards, Donald McLaren
> =================
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital
> and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
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> On Tue, Aug 27, 2013 at 1:08 AM, Cameron Craddock <
> cameron.craddock at gmail.com <javascript:_e({}, 'cvml',
> 'cameron.craddock at gmail.com');>> wrote:
>
>> sounds great to me!
>>
>> -cc
>>
>>
>>
>> On Mon, Aug 26, 2013 at 8:51 PM, Pierre Bellec <
>> pierre.bellec at criugm.qc.ca <javascript:_e({}, 'cvml',
>> 'pierre.bellec at criugm.qc.ca');>> wrote:
>>
>>> Dear hubs,
>>>
>>> I am posting on this list regarding one of the brainhack 2013 (ongoing)
>>> project: quality control (QC) of processed rs-fMRI. I just heard a terrific
>>> talk from Frissoni, and I think what we would want is something like that:
>>> http://www.hippocampal-protocol.net/SOPs/index.php
>>>
>>> Basically
>>> (1) set up a QC form,
>>> (2) get a panel of experts to use it on a large database,
>>> (3) get them to discuss conflicts,
>>> (4) loop until you reach a consensus with more directions on QC choices
>>> (and possibly new QC metrics as well), which you document in a painfully
>>> detailed operations manual.
>>> (5) Then you get an online interface were "naive" people who just read
>>> the manual are presented with test cases to train and eventually certify
>>> that people get it (when they reach a good-enough score).
>>> (6) you grade intra-inter-rater consistency for naive raters that got
>>> through the certification to check that it actually works.
>>> (7) Finally, you test what is the effect of QC on a number of analysis,
>>> to check if it does impact the results (and that it was worth doing all of
>>> that).
>>>
>>> Frissoni, Duchesnes and coll. have done something like that for
>>> hippocampus segmentation instead of QC, and I think this is a really good
>>> way to help standardize the production of imaging outcomes. For the QC, the
>>> same approach could work for a variety of packages, as NIAK/DSPARF/CPAC and
>>> others have a lot of the operations in common, just using different tools.
>>> Results of QC would actually be a great way to compare the
>>> accuracy/robustness of different pipelines (one of the main things we have
>>> examined so far is coregistration T1->stereotaxic and T1->BOLD).
>>>
>>> We have started working on this project with a PhD student, Yassine
>>> Benhajali, in collaboration with some folks at NYU (Cameron Craddock, Chao
>>> Gan Yang, Qingyang Li) as well as Maarten Mennes. This initiative started
>>> at brainhack2012, and has been an important component of the "ABIDE
>>> preprocessed" release (yet-to-come ... but getting there ...). Yassine has
>>> drafted an operation manual that he is revising, and we have a number of
>>> metrics that could be used in the first round of the panel. So we kind of
>>> went through 1-4 once, and we should get a preliminary idea on 7 soon,
>>> while preparing the "ABIDE preprocessed" paper.
>>>
>>> What we need to do next is to get an actual QC report form going (we
>>> just agreed loosely on what to look at for now), ideally web-based, and
>>> update the operation manual. And hopefully build the panel, select a
>>> dataset (which is likely going to remain ABIDE ...) and go through one or
>>> more iteration. If anybody is interested to be part of that, please get in
>>> touch. I am going to post a project description on brainhack.org, but I
>>> prefer to start first with an email on this list in case I get some good
>>> feedback for the project description.
>>>
>>> Sorry about the long post. Best,
>>>
>>> Pierre
>>>
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>>>
>>
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>

-- 
Pierre Bellec, PhD
Researcher / Chercheur, Research Centre of the Montreal Geriatric Institute
Professeur adjoint sous octroi, Department of Computer Science and
Operations Research
University of Montreal, Québec, Canada
1 514 340 3540 #3367
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
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