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  August 2017

FSL August 2017

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Randomise: max F-value positive, but max T is zero for all contrasts

From:

"C.P. Frost" <[log in to unmask]>

Reply-To:

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

Date:

Mon, 28 Aug 2017 22:13:52 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (67 lines)

Hi FSL Experts,

I have what seems like a very basic a problem with several possible causes, though each cause is likely to be very simple.

I'm using randomise to run a simple f-test with white matter FA (via TBSS) across three unequal subject groups. The t-stat maps from randomise -- both corrected and uncorrected -- have minimum and maximum values of (±)0.000000, and most, but not all, have peak voxels of 255 0 0. The f-stats, however, have nonzero (if small: F=9.04, corrp=.237) maximum values at interpretable locations.

Even if there were no significant groupwise differences in FA, it seems implausible that max t-values would be 0.000000, much less if f-stats are nonzero, even if not significant. Is this normal or even axiomatic behavior for randomise when performing an F-test in randomise? And what are the likeliest causes & fixes for this behavior if it's not just a matter of interpretive failure on my part?

I have run various other t-contrasts on this dataset with error-free, interpretable results. I only seem to encounter these issues with f-contrasts.


Input/Output below. NB: groups are low, mild, and severe scores on a subscale of the Childhood Trauma Questionnaire (CTQ).

CTQ.mat:
/NumWaves 3
/NumPoints 75
/Matrix
1 0 0
1 0 0
...
0 0 1

CTQ.con:
/NumWaves 3
/NumPoints 3
/Matrix
1 0 0
0 1 0
0 0 1

CTQ.fts:
/NumWaves 3
/NumPoints 1
/Matrix
1 1 1

randomise options: -i all_FA_skeletonised -o CTQ -m mean_FA_skeleton_mask -d CTQ.mat -t CTQ.con -f CTQ.fts -n 1000 -C .95 -x -V -D
Loading Data:
Data loaded
Warning: Data demeaning selected, but at least one design column has non-zero mean - therefore invoking automatic demeaning of design matrix
3.95489e+28 permutations required for exhaustive test of f-test 1
Doing 1000 random permutations
Starting permutation 1 (unpermuted data)

[...]

Starting permutation 1000
Critical Value for: CTQ_vox_corrp_fstat1 is: 13.0897
5.09921e+20 permutations required for exhaustive test of t-test 1
Doing 1000 random permutations
Starting permutation 1 (unpermuted data)

[...]

Starting permutation 1000
Critical Value for: CTQ_vox_corrp_tstat1 is: 5.47727
Critical Value for: CTQ_clusterm_corrp_tstat1 is: 6152.31 [<--this also seems high...]
5.60659e+14 permutations required for exhaustive test of t-test 2

[similar for t-tests 2 and 3]
Finished, exiting.


Thanks much,
C.P. Frost
UW-Madison

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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


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