Fantastic, thanks for all your help and patience. It is greatly appreciated!
Roger
Quoting Michael Harms <[log in to unmask]>:
> 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
>> >> >> >>>
>> >> >>
>> >>
>> ---------------------------------------------------------------------------
>> >> >> >>>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>
>> >> >> >
>> >> >
>> >>
>> >
>
|