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  July 2012

SPM July 2012

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Explicit/Implicit Masking VBM analysis

From:

Jonathan Peelle <[log in to unmask]>

Reply-To:

Jonathan Peelle <[log in to unmask]>

Date:

Tue, 17 Jul 2012 14:53:07 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (68 lines)

Dear Rayana,

> When pre-processing structural data, I have found a VBM Manual that uses
> DARTEL and a VBM8 Manual that requires downloading the VBM8 toolbox. What is
> the difference between the two, if there is one at all, and are there
> certain conditions when I would use either one? Also, what is the difference
> between the VBM8 toolbox and other cnn toolboxes. I have provided links for
> clarification on what I am talking about.
> http://dbm.neuro.uni-jena.de/vbm8/VBM8-Manual.pdf
> http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf

VBM8 is a toolbox for conducting VBM analyses using SPM (including
DARTEL), but a slightly different approach than the built-in SPM
functions. There is probably not a clear reason to use one or the
other - they are both good approaches. It's worth reading the VBM8
webpage to understand some of the differences. I'm not aware of any
studies directly comparing the results.


> My second question deals with the implicit/explicit masking options given
> under the analysis. When would I include an explicit mask? I also notice the
> default is to include an implicit mask? How do either of these have an
> effect when I want to analyze the structural scans?

Masks will limit the voxels included in your analysis. Let's say that
you are only interested in left frontal cortex in your VBM study; if
you had a mask of this region, including it as an explicit mask would
be one way to focus your analysis here. Another common reason to use
an explicit mask is to restrict analyses to "gray matter" - although
using a threshold mask (as you mention) often does a very reasonable
job of this, so it's not really necessary (but some people prefer the
explicit mask approach).


> My last question is about the threshold masking. The default "specify value"
> option is 100 but the manuals I have looked at recommend either 0.1 or 0.2.
> Which is the best to use and why (I know it might depend on the
> circumstances).

For an absolute threshold, the number will depend on the kind of data
being entered. For functional MRI data this will be different than
structural MRI data. The recommendations of something like 0.1 or 0.2
reflect that most values for structural MRI data are based on
probabilities, and so lie between 0-1 (although if images are
modulated, perhaps a bit greater than 1). There is no clear standard
here - the idea is to exclude things that are unlikely to be brain.
Empirically 0.1 and 0.2 work well for many people. You can try this
both ways, and compare the resulting mask.img - this will give you an
idea of the areas that differ, and what is being masked out. (For fun,
you could also try it with a threshold of 0.9, or with no threshold
masking, and then you can see the value of including this mask.)

Hope this helps!

Best regards,

Jonathan

-- 
Dr. Jonathan Peelle
Center for Cognitive Neuroscience and
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104
USA
http://jonathanpeelle.net/

Top of Message | Previous Page | Permalink

JISCMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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