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  June 2015

SPM June 2015

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Effect size

From:

"Angstadt, Mike" <[log in to unmask]>

Reply-To:

Angstadt, Mike

Date:

Thu, 11 Jun 2015 20:33:39 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

Aser,



You’ll need to use elementwise division operations (./) on the standard error since both numerator and denominator are matrices. And the denominator for the effect size should just be sqrt(degree of freedom) according to the linked PDF.



So effect size select the T image and use:

(i1*2)/(sqrt(degree of freedom))



Standard error select the T image and the con image in that order and use:

i1./i2



-Mike



From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Aser A

Sent: Thursday, June 11, 2015 2:52 PM

To: [log in to unmask]

Subject: Re: [SPM] Effect size



Thanks Donald. 



Ah! I thought the contrast is the effect size or at least maybe some papers refer to it. It is also mentioned in this link : http://www.fil.ion.ucl.ac.uk/spm/doc/manual/results.htm 



You mentioned that it does plot the amplitude. So I am confused now between the contrast estimate, effect size and the amplitude ? What do them mean and represent? 





Also from a practical point of view, If I enter the SPMT_0001.nii (or the t value maps) in imcalc and use this expression to calculate:



 The effect size = (i1*2)/(sqrt(degree of freedom-1))



Then If I want to calculate the standard error I would enter both the t map and the con image and use the following expression : i1/i2 



Are these practical steps correct to reach and calculate a map of the effect size and the standard error?



Many thanks



Aser





On Thu, Jun 11, 2015 at 6:57 PM, MCLAREN, Donald <[log in to unmask]> wrote:

Aser,



SPM does not plot, at least to my knowledge, the effect size (http://en.wikipedia.org/wiki/Effect_size). It does plot the amplitude, but amplitude is not the effect size.



The amplitude is just the value of the contrast image.



The standard error is the value of the T-image divided by the value of the contrast image. Alternatively, you could use: sqrt(diag(SPM.xCon(Ic).c'*ResMS*SPM.xX.Bcov*SPM.xCon(Ic).c)).



You can also compute the effect size directly from the T-map, the following link has come common formulas for computing the effect size from statistical values:

http://www.soph.uab.edu/Statgenetics/People/MBeasley/Courses/EffectSizeConversion.pdf



Hope this helps.





Best Regards, Donald McLaren

=================

D.G. McLaren, Ph.D.

Research Fellow, Department of Neurology, Massachusetts General Hospital and

Harvard Medical School

Postdoctoral Research Fellow, GRECC, Bedford VA

Website: http://www.martinos.org/~mclaren

Office: (773) 406-2464

=====================

This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED

HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is

intended only for the use of the individual or entity named above. If the

reader of the e-mail is not the intended recipient or the employee or agent

responsible for delivering it to the intended recipient, you are hereby

notified that you are in possession of confidential and privileged

information. Any unauthorized use, disclosure, copying or the taking of any

action in reliance on the contents of this information is strictly

prohibited and may be unlawful. If you have received this e-mail

unintentionally, please immediately notify the sender via telephone at (773)

406-2464 or email.



On Thu, Jun 11, 2015 at 1:05 PM, fMRI <[log in to unmask]> wrote:

Thanks



I am still lost. Is the images that you are talking about the con images. Or in other words, using SPM plot contrast estimate, it plots the size effect with the standard error at this selected voxel and also creates and a mat called contrast which bas the values at this coordinates. All what I want to do is to try to find a way , e.g using imcalc, to generate this for list of coordinates. I am still not sure how I can do it.



Regards,



A



Regards,



AS

> On 11 Jun 2015, at 15:31, "H. Nebl" <[log in to unmask]> wrote:

>

> With Imcalc you can conduct operations like mean(X), std(X) based on a series of volumes, resulting in a 3D volume with corresponding values on a voxel-by-voxel basis. You have to go with "Yes - read images into data matrix".

>

> Best

>

> Helmut





**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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