Hackathon project: updating diagnostic toolbox for SPM

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Remi Gau

Nov 4, 2021, 3:12:55 AM11/4/21
to NIQC, Thomas Nichols, Isil Bilgin

Hey NIQC experts,

For the coming brainhack global, we're trying to find some projects that could related to some of the "big softwares" in our field.

I got in touch with Tom Nichols regarding the possibility to update the "SPM diagnosis" toolbox that provide a way to do quality control of fMRI models in visual way by checking the validity of inferences in fMRI modeling, and characterizing fMRI signal and artifacts through exploratory data analysis (example of visual reports).

Currently the toolbox does not run on SPM12 so the main goal of this project would be to "just" make the toolbox run on SPM12. The project could also plant seeds to give ideas to develop similar tools in python and for other analysis software.
I tend to feel that there is quite a need for this type of tool in the community.

The thing is that neither Tom (nor I) have the bandwidth to lead that project alone, so we are trying to see if we can get a small group of people to help co-lead this project.

So I am writing to see if some of you would like to help with this (or know of people who could be interested in this). It could also be an entrypoint for people who would like to join and contribute to the Brainhack community.

What do you say ?



Rémi Gau

JB Poline

Nov 4, 2021, 10:21:05 AM11/4/21
to Remi Gau, NIQC, Thomas Nichols, Isil Bilgin
I wonder if it might not be a better move to start sketching a python "nipyqc" directly - I can ask a couple of students who might be interested in this

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Raamana, Pradeep Reddy

Nov 4, 2021, 10:34:18 AM11/4/21
to jbpo...@gmail.com, Remi Gau, NIQC, Thomas Nichols, Isil Bilgin
I’d also strongly we recommend we separate QC / diagnostic tools from the preprocessing tools, that we can have a tool-agnostic definitions / consensus for issues etc. unless this is a very SPM-specific thing! 😀

Regarding visual reports, I haven’t reviewed the linked article yet, but if there is a way customize visualQC (which already helps with some multi-layered review of fMRI data) to achieve them, I’d be happy to help contribute. 

From: ni...@googlegroups.com <ni...@googlegroups.com> on behalf of JB Poline <jbpo...@gmail.com>
Sent: Thursday, November 4, 2021 10:20:52 AM
To: Remi Gau <remi...@gmail.com>
Cc: NIQC <ni...@googlegroups.com>; Thomas Nichols <thomas....@bdi.ox.ac.uk>; Isil Bilgin <bilg...@gmail.com>
Subject: Re: [niQC] Hackathon project: updating diagnostic toolbox for SPM

Remi Gau

Nov 4, 2021, 11:03:45 AM11/4/21
to Raamana, Pradeep Reddy, jbpo...@gmail.com, NIQC, Thomas Nichols, Isil Bilgin

I don't see the 2 approaches as being incompatible: definitely makes sense to try to build python tools / better to have a tool-agnostic approaches AND check what already exist to see what we want to those python tools to do.


Rémi Gau

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