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:

Monospaced Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  September 2007

SPM September 2007

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: SVC

From:

Douglas Burman <[log in to unmask]>

Reply-To:

Douglas Burman <[log in to unmask]>

Date:

Fri, 7 Sep 2007 15:20:57 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (131 lines)

This thread has gone on so long that I may not remember correctly what
prompted it. If my memory does serve correctly, I may be able to shed some
light.

As I remember, a question was raised about differences in activation
observed when a ROI was specified before brain analysis was begun (thereby
including only the ROI voxels in analysis) vs. the activation when the SVC
correction is applied, which is supposed to limit the analysis to voxels in
the ROI. The latter condition was found (I think) to depend on the default
values set for the whole-brain analysis, even though the SVC limits its
statistics to voxels within the ROI.

Briefly, differences in outcome result from the process of identifying
baseline brain activity. If a model is used that includes the whole-brain
analysis before pressing the SVC button, the baseline is determined from
the mean activity and variance across all the voxels in the brain, which is
then used to obtain beta values for each voxel. SVC then limits its
statistical analysis to those beta values to those voxels within the ROI.

If the original model for analysis is instead limited to the ROI (such as
occurs when selecting a ROI during analysis with PickAtlas), the baseline
is determined only from the mean activity and variance of voxels within the
ROI. This results in different beta estimates for each voxel, thereby
producing different statistical outcomes despite the fact that the final
statistical analyses in both cases is limited to the ROI.

I will spare you the details of how I came to this understanding.

Doug

At 04:55 PM 9/7/2007 +0100, Ged Ridgway wrote:
>Hello,
>
>Perhaps my last email on this topic wasn't as concise or clear as it
>perhaps should have been, but I remain to be convinced that it's
>incorrect... though like Marko said, I too may be utterly wrong, in which
>case hopefully someone will clarify, with reference to the code, what is
>actually happening.
>
>However, Mahinda, I think your observation can be explained consistently
>with what Susie and I seemed to find, and what I described previously.
>
>>>Following from the recent SVC discussion I was under the impression that
>>>the SVC when applied only includes those voxels (within whatever volume
>>>you have defined) that were initially activated at the previously chosen
>>>uncorrected threshold. In which case the value chosen for this
>>>threshold should dictate the number of voxels within the region where
>>>the SVC is applied and therefore also the resulting p value for the analysis.
>
>This is an extremely good point, which I hadn't thought about properly.
>But returning to the code, I think the explanation can be seen in the
>following lines from spm_VOI.m:
>
> 122 xSPM.S = length(k);
> 123 xSPM.R = spm_resels(FWHM,D,SPACE);
> 124 xSPM.Z = xSPM.Z(j);
> 125 xSPM.XYZ = xSPM.XYZ(:,j);
> 126 xSPM.XYZmm = xSPM.XYZmm(:,j);
> 127 xSPM.Ps = xSPM.Ps(k);
>
>As I described in my previous email,
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708&L=SPM&P=16990
>the variables k and j come respectively from the complete set of voxels in
>the SVC ROI, and the subset in both the ROI and the set of whole-brain
>supra-threshold voxels.
>
>Now, in lines 122 and 123 we see that the size of the search volume, in
>voxels and resels, uses the entire SVC ROI (respectively through k, and
>then directly in the spm_resels function). Similarly, line 127 stores the
>sorted p-values used for any subsequent FDR correction using the complete
>ROI set, k.
>
>(For FDR, note that in spm_getSPM, line numbering from SPM5 latest
>updates, we find
> 533 % P values for False Discovery FDR rate computation
> % (all search voxels)
> 545 %-Compute mask and eliminate masked voxels
>that indeed Ps is independent of the whole-brain threshold used in lines
>545 onward.)
>
>So, the previous whole-brain threshold affects (in my/Susie's opinion) the
>set of voxels which are considered (through line 124-126 above, with the
>subset of voxels j), but not the characterisation of either the search
>volume for FWE or the p-value distribution for FDR. So the significance of
>the *reported* voxels won't depend on the previous whole-brain threshold,
>but some voxels might not be reported at all, if the whole-brain threshold
>was too strict.
>
>Mahinda, if you vary the uncorrected whole-brain threshold from the values
>of 0.99 and 0.01 that you mentioned in your previous email, down to 0.001,
>0.0001, 0.00001, etc. do you still find that the SVC is independent of
>this prior threshold, or do the voxels disappear from the results (even
>though those voxels that remain show unchanged significance)? This would
>be interesting to know. If so, I'd like to ask again the questions in my
>previous email:
>- whether this is deliberate/correct
>- if so why
>- and if for good reason, does the practice of setting the whole-brain
>alpha near to one violate that reason?
>
>And if not, please do tell the mailing list, so that people can throw
>rotten vegetables at me when they next see me ;-)
>
>>I would see no good rationale for excluding voxels within the search
>>volume on the basis of an analysis that you are not interested in anyway
>
>Nor can I, Marko, but this is what Susie seemed to find was happening in
>practice, and what matched my interpretation of the code. And this:
>
>>but there may be factors involved that I do not see
>
>is worrying me too... Hopefully other more knowledgeable folk can comment
>on this...
>
>All the best,
>Ged.
>
>P.S. I fear this email is also not "as concise or clear as it perhaps
>should" be... Sorry about that. But perhaps I could borrow Blaise Pascal's
>famous apology: "Je n'ai fait celle-ci plus longue que parceque je n'ai
>pas eu le loisir de la faire plus courte." -
>http://en.wikiquote.org/wiki/Blaise_Pascal

Dept. of Communication Sciences & Disorders
Northwestern University
2240 Campus Drive
Frances Searle Building, Room 2-356
Evanston, IL 60208
phone 847-467-1549
fax 847-491-4975
email: [log in to unmask]

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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


WWW.JISCMAIL.AC.UK

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