Hi Michael
Thanks for your reply.
So to "control for" IQ, I need to take the mean IQ from the entire sample and
substract it from indiviual subjects IQ and use these values as the
demeaned IQ
for each subject?
Otherwise, can you please let me know if the design.con and design.mat
files in
my previous email are set up correctly?
Thanks again. Your help in very much appreciated!
Roger
Quoting Michael Harms <[log in to unmask]>:
> 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
>> >>>
>> ---------------------------------------------------------------------------
>> >>>
>> >>>
>> >>>
>> >>>
>> >>
>> >
>
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