JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives


SPM Archives

SPM Archives


SPM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  May 2014

SPM May 2014

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Second level bayesian modelling - Activation threshold = 0?

From:

"Penny, William" <[log in to unmask]>

Reply-To:

Penny, William

Date:

Thu, 29 May 2014 09:41:06 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

Dear Peter, Glad et al,



This is great advice from Glad below.



It's probably worth adding that Bayesian inference at the 2nd level is considerably quicker (eg just a few minutes, possibly tens of minutes)



The main reason for this is that there are usually many fewer images than at the first level - tens rather than hundreds.



The procedure here is to Specify a 2nd level model - t-tests, ANOVA etc - then estimate it with the Classical option

(you can also play with some contrasts here).  Then estimate the model again using the Bayesian 2nd level option and you can create parameter inference and model comparison maps [1] by specifying contrasts in the usual way.

Its perfectly valid to compare parameters to a threshold of zero.



Importantly, the data going into this analysis can be any set of con*.images from a first level analysis - ie from the usual classical SPM first level model. You don't have to also do Bayesian analysis at the first level.



If you're going to HBM this year, you might like to come to the education session on the Sunday - I'll be giving a talk on PPMs.



All the best,



Will.



[1] W. Penny and G. Ridgway (2013). Efficient Posterior Probability Mapping using Savage-Dickey Ratios. PLoS One 8(3), e59655







> -----Original Message-----

> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]

> On Behalf Of Paul Glad Mihai

> Sent: 29 May 2014 09:42

> To: [log in to unmask]

> Subject: Re: [SPM] Second level bayesian modelling - Activation threshold =

> 0?

> 

> Dear Peter,

> 

> Bayesian inference has some advantages over the frequentist approach (also

> termed classical for some reason, but classical statistics is even older than

> frequentist statistics... that's another topic):

> 

> * you don't have to correct for multiple comparisons, although some might

> disagree (see Woolrich 2012, Neuroimage)

> * your answer will be a probability that the effect is there given the data, as

> opposed to rejecting the null hypothesis given a small enough p-value

> * with frequentist inference having a lot of data or sensitivity can declare an

> activation for every voxel in the brain, i.e. it will reject the null hypothesis for

> for every voxel in the brain

> * in SPM for first level Bayesian inference a spatial regularization prior is used

> on the unsmoothed data, meaning that the smoothing is automatic -- a much

> better approach than smoothing with a fixed width kernel over the whole

> brain

> * you can compare non-nested models, something you can't do with

> frequentist inference (Rosa, 2010 Neuroimage; Harrison, 2011; Frontiers in

> Human Neuroscience)

> 

> If you look at the examples in the SPM manual will get a bit of an idea of the

> steps you need to take in Bayesian inference in SPM. However it doesn't tell

> you much about 2nd level inference. Regardless, I would suggest you go

> through those examples step by step. What you will find, and what I found

> was that Bayesian inference finds expected activations where the

> frequentist approach doesn't -- so you could say it is more specific, although

> that's not really a right term to use in Bayesian statistics.

> 

> The biggest drawback is the long computation time. Just to give you an idea,

> on an 8 core intel i5 with 8 parallelized processes it took around

> 26 hours for 51 subjects with one session each for the first level Bayesian

> estimation. Mind you I also asked for the log model evidence.

> 

> To get an idea of Bayesian inference I would first suggest you look at the

> videos on the SPM website, specifically:

> http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG_Bayes

> http://www.fil.ion.ucl.ac.uk/spm/course/video/#Bayes

> 

> I would watch both!

> Concerning reading material you can take a look at the SPM book chapters

> 22,23 maybe 24 and maybe 25. The latter two are maths heavy. You can find

> some of the PDFs on the SPM website

> http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/

> 

> If you need a general overview of Bayesian statistics then check out

> Kruschke's Doing Bayesian Data Analysis or his video on it:

> http://www.indiana.edu/~video/stream/launchflash.html?format=mp4&fol

> der=ssrc&filename=2012-10-05_wim_kruschke_bayesian.mp4

> 

> And if you really want to get into Bayesian statistics then check out David

> Draper's video lectures and exercises:

> http://users.soe.ucsc.edu/~draper/eBay-Google-2013.html

> 

> And last but not least, the scholaropedia entry for Bayesian statistics is nice

> and short:

> http://www.scholarpedia.org/article/Bayesian_statistics

> 

> I hope this helps!

> 

> Have fun with Bayes!

> 

> Glad

> 

> On 29.05.2014 01:02, SPM automatic digest system wrote:

> > Date:    Tue, 27 May 2014 23:34:09 +0000

> > From:    Peter Goodin <[log in to unmask]>

> > Subject: Second level bayesian modelling - Activation threshold = 0?

> >

> > Hi SPM list,

> >

> > I'm doing a second level analysis on my fmri data and have been reading

> about the Bayesian method, which for my interests has been suggested to

> be robust to the effects of outliers (is this true)?

> >

> > Having a read through the mailing list I see that the initial PPM threshold

> doesn't have to be used but I was wondering if it's acceptable to have y = 0?

> >

> > Can anyone recommend some further reading on the pros and cons of low

> threshold PPMs?

> >

> > Thanks,

> >

> > Peter

> 

> --

> Glad MIHAI, M.Sc. Biomedical Physics

> Functional Imaging | University Clinic Greifswald Walther-Rathenau-Stra├če 46

> | 17475 Greifswald | Germany

> Tel: +49 3834 86 69 44 | Fax: +49 3834 86 68 98 www.baltic-imaging-center.de



Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager