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  November 2011

FSL November 2011

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: TBSS, 2 groups, controlling for IQ

From:

Michael Harms <[log in to unmask]>

Reply-To:

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

Date:

Wed, 23 Nov 2011 10:28:30 -0600

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (252 lines)

If you want to do an analysis in which you look for a main effect of IQ
across all subjects, then you should also demean across all subjects --
not separately demean the controls and patients.  See Jeanette Mumford's
web page.

cheers,
-MH

On Wed, 2011-11-23 at 09:40 -0500, Roger Jou wrote:
> Hi Dave,
> 
> Thanks so much for your reply.  I just wanted double check that I have this
> right.  Below I have IQ scores in the left column and demeaned IQ 
> scores in the
> right column.  The first 11 rows are controls and the remaining 19 rows are
> patients.  For the demeaned values for controls and patients, I 
> calculated this
> by [individual control IQ – control mean IQ] and [individual patient IQ –
> patient mean IQ], respectively.
> 
> 106 -8.4
> 127 12.6
> 131 16.6
> 114 0.1
> 117 2.6
> 92 -22.4
> 113 -1.4
> 123 8.6
> 111 -3.4
> 110 -4.4
> 114 -.4
> 127.0 35.7
> 107 15.7
> 102 10.7
> 100 8.7
> 86 -5.3
> 51 -40.3
> 114 22.7
> 108 16.7
> 80 -11.3
> 76 -15.3
> 78 -13.3
> 90 -1.3
> 85 -6.3
> 100 8.7
> 93 1.7
> 121 29.7
> 84 -7.3
> 41 -50.3
> 91 0.1
> 
> If this is correct, then are the followng design.con and design.mat files
> correct?
> 
> design.con file:
> 
> /NumWaves 3
> /NumContrasts 2
> /PPheights 1 1
> /Matrix
> 1 -1 0
> -1 1 0
> 
> design.mat file:
> 
> /NumWaves 3
> /NumPoints 30
> /PPheights 86 86
> /Matrix
> 1 0 -8.4
> 1 0 12.6
> 1 0 16.6
> 1 0 0.1
> 1 0 2.6
> 1 0 -22.4
> 1 0 -1.4
> 1 0 8.6
> 1 0 -3.4
> 1 0 -4.4
> 1 0 -0.4
> 0 1 35.7
> 0 1 15.7
> 0 1 10.7
> 0 1 8.7
> 0 1 -5.3
> 0 1 -40.3
> 0 1 22.7
> 0 1 16.7
> 0 1 -11.3
> 0 1 -15.3
> 0 1 -13.3
> 0 1 -1.3
> 0 1 -6.3
> 0 1 8.7
> 0 1 1.7
> 0 1 29.7
> 0 1 -7.3
> 0 1 -50.3
> 0 1 0.1
> 
> Also, I wanted to double check that the PPheights are the difference 
> between the
> most negative and most positive demeaned IQ for the entire sample.
> 
> Finally, in order to run this would the procedure be the same as that 
> indicated
> on the main TBSS documentation page, except using the above for the for the
> design.mat and design.con files below:
> 
> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d 
> design.mat
> –t design.con -n 1000 --T2 –V
> 
> Thanks so much your kind assistance!
> 
> Roger
> 
> 
> Quoting David Flitney <[log in to unmask]>:
> 
> > Simply put your raw IQ scores into one column, demean as one, and 
> > drop the last column in your contrasts list. This will allow you to 
> > model the linear effect of IQ(?) on your expected signal... but 
> > spread the misfit across your signal in a unpredictable way if this 
> > is not the case.
> >
> > --
> > Dave Flitney
> > IT Manager, FMRIB Centre
> >
> > On 22 Nov 2011, at 17:37, Roger Jou <[log in to unmask]> wrote:
> >
> >> Dear Prof Smith,
> >>
> >> Thank you for clarifying my error.  I understand what this means 
> >> conceptually,
> >> but could please show me what the design.con and design.mat looks 
> >> like?  I want
> >> to be certain I am on the right track.  Thanks again.
> >>
> >> Regards,
> >>
> >> Roger
> >>
> >> Quoting Stephen Smith <[log in to unmask]>:
> >>
> >>> Hi - no this is incorrect - if you want to "control for" IQ this 
> >>> needs to be a single EV (across both groups) that will attempt to 
> >>> model out the effect of IQ.
> >>> However that will only succeed (ie remove this confound in the 
> >>> group difference) to the extent that the effect of IQ on the data 
> >>> is linear and additive - which cannot necessarily be assumed.
> >>> Cheers.
> >>>
> >>>
> >>> On 19 Sep 2011, at 19:42, Roger Jou wrote:
> >>>
> >>>> Dear FSL Experts,
> >>>>
> >>>> I am conducting a TBSS analysis on FA, MD, AD and RD and plan to 
> >>>> use TFCE.  The study consists of two groups (control = 11 and 
> >>>> patient = 19) who differ significantly in IQ.  Therefore, I wanted 
> >>>> conduct the analysis controlling for IQ and would be extremely 
> >>>> grateful for help in generating the appropriate design.con and 
> >>>> design.mat files.
> >>>>
> >>>> I have looked through the forum for answers and have drafted the 
> >>>> following:
> >>>>
> >>>> design.con
> >>>>
> >>>> /NumWaves 4
> >>>> /NumContrasts 2
> >>>> /PPheights 1 1
> >>>> /Matrix
> >>>> 1 -1 0 0
> >>>> -1 1 0 0
> >>>>
> >>>> Can you please tell me whether this design.con file is correct?
> >>>>
> >>>> design.mat
> >>>>
> >>>> /NumWaves 4
> >>>> /NumPoints 30
> >>>> /PPheights 86 86
> >>>> /Matrix
> >>>> 1 0 -8.4 0
> >>>> 1 0 12.6 0
> >>>> 1 0 16.6 0
> >>>> 1 0 0 0
> >>>> 1 0 2.6 0
> >>>> 1 0 -22.4 0
> >>>> 1 0 -1.4 0
> >>>> 1 0 8.6 0
> >>>> 1 0 -3.4 0
> >>>> 1 0 -4.4 0
> >>>> 1 0 -0.4 0
> >>>> 0 1 0 35.7
> >>>> 0 1 0 15.7
> >>>> 0 1 0 10.7
> >>>> 0 1 0 8.7
> >>>> 0 1 0 -5.3
> >>>> 0 1 0 -40.3
> >>>> 0 1 0 22.7
> >>>> 0 1 0 16.7
> >>>> 0 1 0 -11.3
> >>>> 0 1 0 -15.3
> >>>> 0 1 0 -13.3
> >>>> 0 1 0 -1.3
> >>>> 0 1 0 -6.3
> >>>> 0 1 0 8.7
> >>>> 0 1 0 1.7
> >>>> 0 1 0 29.7
> >>>> 0 1 0 -7.3
> >>>> 0 1 0 -50.3
> >>>> 0 1 0 0
> >>>>
> >>>> Can you please tell me whether this design.mat file is correct?
> >>>>
> >>>> Also, I wanted to double check that the PPheights are the 
> >>>> difference between the most negative and most positive demeaned IQ 
> >>>> for the entire sample, and the IQ needs to be demeaned separately 
> >>>> for control and patient groups.
> >>>>
> >>>> Finally, in order to run this would the procedure the same as that 
> >>>> indicated on the main TBSS documentation page, just using the 
> >>>> above for the for the  design.mat and design.con files below:
> >>>>
> >>>> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask 
> >>>> -d design.mat -t design.con -n 500 --T2 -V
> >>>>
> >>>> Thanks in advance for your help!
> >>>>
> >>>> Roger
> >>>>
> >>>
> >>>
> >>> ---------------------------------------------------------------------------
> >>> Stephen M. Smith, Professor of Biomedical Engineering
> >>> Associate Director,  Oxford University FMRIB Centre
> >>>
> >>> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> >>> +44 (0) 1865 222726  (fax 222717)
> >>> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> >>> ---------------------------------------------------------------------------
> >>>
> >>>
> >>>
> >>>
> >>
> >

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
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


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

For help and support help@jisc.ac.uk

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