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FSL  November 2011

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Subject:

Re: TBSS, 2 groups, controlling for IQ

From:

Roger Jou <[log in to unmask]>

Reply-To:

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

Date:

Tue, 22 Nov 2011 12:37:00 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (114 lines)

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
> ---------------------------------------------------------------------------
>
>
>
>

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