Yes, that model would be appropriate for testing for a group difference
while controlling for the linear effect of a covariate that applies to
all subjects (w/o regard to group status).
cheers,
-MH
>On Wed, 2011-11-23 at 12:25 -0500, Roger Jou wrote:
> Great, thanks again Michael! Just one last thing: can you please look
> over the
> below design.con and design.mat setups? Provided that the demean column (3rd)
> in the design.mat is calculated using mean from entire sample, are these
> correctly set up? Again thank you very much.
> Roger
>
> 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
>
>
> Quoting Michael Harms <[log in to unmask]>:
>
> > Yes, use the mean from the entire sample.
> >
> > On Wed, 2011-11-23 at 11:55 -0500, [log in to unmask] wrote:
> >> 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
> >> >> >>>
> >> >>
> >> ---------------------------------------------------------------------------
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>
> >> >> >
> >> >
> >>
> >
|