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

Help for FSL Archives


FSL Archives

FSL Archives


FSL@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

FSL Home

FSL Home

FSL  July 2007

FSL July 2007

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Group comparisons of Melodic Components

From:

Peter Fried <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 9 Jul 2007 08:30:31 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (92 lines)

Thanks so much!
-Pete

> Hi Peter,
>
>> I've collected resting-state fmri data from a patient group and a
>> control
>> group. After processing the data using the pre-stats tab in FEAT and
>> subsequently running MELODIC, I merged the subjects' melodic outputs
>> together and reran MELODIC. From the resulting output, I've
>> indentified a
>> number of components of interest that I'd like to compare between
>> the two
>> groups.
>
>> My understanding of what I should do is the following:
>>
>> 1) Create a mask representing the combined thresh_zstat maps for
>> both groups.
>
> nothing wrong with this, but you won't need it later
>
>> 2) Concatenate all the thresh_zstat maps of a particular component
>> for all
>> subjects, with all the subjects in one group first, followed by all
>> the
>> subjects in the second.
>>
>
> No, you wouldn't want to run any model based higher-level analysis on
> thresholded lower-level stats images - simply use the associated
> unthresholded maps instead.
>
>
>> 3) Create design.mat and design.con files using the GLM Setup utility,
>> where my design looks like the following:
>>     group    EV1     EV2
>>             groupA  groupB              Title      EV1    EV2
>> s1   1         1      0       | C1   groupA mean    1      0
>> s2   1         1      0       | C2   groupB mean    0      1
>> s3   1         1      0       | C3      A > B       1     -1
>> s4   1         1      0       | C4      B > A      -1      1
>> s5   2         0      1       |
>> s6   2         0      1       |
>> s7   2         0      1       |
>> s8   2         0      1       |
>>
>
> That sounds OK
>
>> 4) run a Two-Sample Unpaired T-test using RANDOMISE with the following
>> command:
>>
>> randomise -i <4D_input> -o <output> -d design.mat -t design.con -c
>> 0.99
>>
>
> nope, the argument to the -c (or -C) option is in units of the raw t-
> stats (not z) that is being formed within randomise, i.e. if you want
> a cluster forming threshold of t>2.3 use that number here. The output
> file contains the p-values, i.e. you can threshold that one at 0.99,
> say after having obtained it from randomise.
> hope this helps
> christian
>
>
>
>> Here are my questions:
>> Does it appear I am setting up the design correctly?
>> Is using the option "-c 0.99" the equivalent of looking for
>> significance
>> at p<0.01?
>> Do you have any other suggestions or recommendations for carrying
>> this out?
>>
>> You help is greatly appreciated. Thanks in advance.
>>
>> Cheers,
>>
>> Pete
>>
>> Center for Magnetic Resonance Research
>> University of Minnesota
>
> ____
> Christian F. Beckmann
> University Research Lecturer
> Oxford University Centre for Functional MRI of the Brain (FMRIB)
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> [log in to unmask]	http://www.fmrib.ox.ac.uk/~beckmann
> tel: +44 1865 222551			fax: +44 1865 222717
>

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


WWW.JISCMAIL.AC.UK

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