Hi All,
Thanks for the great comments here. Martin, I presume this is the link
to the toolbox you are referring to at the end of your message?
https://github.com/rsagroup/rsatoolbox
I will also add to the mix Variational RSA for another perspective on
the topic from an SPM viewpoint:
https://www.sciencedirect.com/science/article/pii/S1053811919305610
Best regards,
Guillaume.
On 26/01/2022 15:48, Martin Hebart wrote:
> ⚠ Caution: External sender
>
>
> Hi Maxime,
>
> I'm an author of TDT and even though I'm really happy if you use it (and
> thanks Tibor for the kind words!), I think there are definitely things
> that need to be improved for RSA for version 4.0 of the toolbox. For
> getting RDMs from brain data, it should really be quite straightforward
> with TDT, specifically for crossnobis distance. Also, running basic RSA
> should work out of the box (e.g. getting the correlation of a model RDM
> with brain RDMs). The devil lies in the detail though: do you want to
> average data of the same conditions, do you want to do cross-validation,
> what distance metric, what comparison, multiple regression, do you want
> to use all cells of the matrix or only some, etc. etc. People on the
> support forum are seem to be most confused about RSA, and it's probably
> because there are so many ways to do it and our toolbox has adopted
> these methods over time. I doubt it would be a lot easier with other
> Matlab-based tools but I just wanted to mention it might take a bit of
> time. I try answering questions in the forum though. :)
>
> If you are firm in Python and like object oriented stuff, it might also
> be worth looking into the new RSA toolbox.
>
> Best,
> Martin
>
> Am Mi., 26. Jan. 2022 um 16:15 Uhr schrieb Auer, Tibor
> <[log in to unmask] <mailto:[log in to unmask]>>:
>
> Hi Maxime,
>
> The Cambridge tool is solid, but I would hesitate to pick a new tool
> without detailed documentation and support.
>
> I have previously used CoSMoMVPA (https://www.cosmomvpa.org
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cosmomvpa.org%2F&data=04%7C01%7Cg.flandin%40UCL.AC.UK%7Cdb1638df917241873f7408d9e0e34de5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637788089137886653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=brDCJm8%2FpJjFBsqp57qcH%2B%2BgdvRa%2FO14mknl4gAjo7U%3D&reserved=0>),
> which is easy to use and have an active user group. I have also
> integrated it in Automatic Analysis
> (https://github.com/automaticanalysis/automaticanalysis) to
> facilitate adoption, and I also have an example pipeline for RSA ,
> which I have not published yet.
>
> I have recently used TDT, which seems the best and most solid of
> all, and an active community is certainly a plus. I have also
> integrated TDT in Automatic Analysis for all sorts of inputs
> (voxel-based, ROI-based, connectivity); however, I have not used it
> for RSA, yet, but it seems straightforward to do it.
>
> Kind regards,
> Tibor
>
> Auer, Tibor M.D. Ph.D.
> Research Fellow
> School of Psychology, Faculty of Health and Medical Sciences
> University of Surrey, Guildford GU2 7XH
> [log in to unmask] <mailto:[log in to unmask]>
> @TiborAuer
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) <[log in to unmask]
> <mailto:[log in to unmask]>> On Behalf Of Maxime Carri ere
> Sent: Wednesday, January 26, 2022 12:46 PM
> To: [log in to unmask] <mailto:[log in to unmask]>
> Subject: [SPM] Representational Similarity Analysis || Where to start?
>
> Hello everyone,
>
>
>
> I have just started my PhD and I have been asked to do
> Representational Similarity Analysis with fMRI. However, there is no
> one in the lab who is working on this technique.
>
> I would like to ask you if you know any good ressources and/or
> package for this purpose? I already selected a couple and your
> opinion would be greatly appreciated!
>
> (1) The Decoding Toolbox
> https://sites.google.com/site/tdtdecodingtoolbox/
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Ftdtdecodingtoolbox%2F&data=04%7C01%7Cg.flandin%40UCL.AC.UK%7Cdb1638df917241873f7408d9e0e34de5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637788089137886653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XgSkbLQP25bkgaYIbeOxk9iO0FAGbHvf%2Bzhzzz2as00%3D&reserved=0>
> With a relatively active community on https://neurostars.org/
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fneurostars.org%2F&data=04%7C01%7Cg.flandin%40UCL.AC.UK%7Cdb1638df917241873f7408d9e0e34de5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637788089137886653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=wpjk5qb5uT%2F96tfJoagYiy7RcuIz7Iwnff3atywuFGA%3D&reserved=0>
>
> (2) The Cambridge Toolbox
> https://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mrc-cbu.cam.ac.uk%2Fmethods-and-resources%2Ftoolboxes%2F&data=04%7C01%7Cg.flandin%40UCL.AC.UK%7Cdb1638df917241873f7408d9e0e34de5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637788089137886653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=T73kdJyoBzLnJn7EYcpOsKJw%2FCT2AUbY3gr6BLvBHwQ%3D&reserved=0>
> However, I could not find any active community.
>
> If you have any other Toolbox, package, or ressources please share ;)
>
> Have a nice day,
>
> Maxime
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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