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