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

[Cameron Craddock]

sounds great to me!

-cc



On Mon, Aug 26, 2013 at 8:51 PM, Pierre Bellec
<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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