On 08/31/2017 02:30 PM, Martin Juneja wrote: > Hi experts, > > I have a follow up question: > In case I wanted to add another covariate in contrast matrix e.g. in > addition to age and gender if I want to add BMI as another covariate > in calculating correlation between volume and LGI (as mentioned in > previous email), could you please confirm if following contrast matrix > is correct: > > *0 0 0 0 0 0 1* > that is correct > for FSGD: > > GroupDescriptorFile 1 > > Class Male > > Class Female > > Variables Age BMI > > Input zerek1 Male 21 17 > > Input zerek2 Male 25 19 > > etc. > > If that's the correct matrix, could you please briefly explain how > this matrix explains the effect of age, sex and BMI i.e. how does each > zero and 1 explain the correlation between volume and LGI and removes > the effect of age, sex and BMI? This is a contrast matrix, so it does not explain anything. It is the columns in the design matrix that will explain effects. Each column means something and each column gets a regression coefficient. By setting the corresponding value in the contrast mat to 0 you tell mri_glmfit to to fit/account for that column in the design but do not include it in the contrast > > Thanks. > > On Tue, May 16, 2017 at 8:31 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > The 2nd is the correct matrix > > > On 5/15/17 12:36 PM, Sahil Bajaj wrote: >> >> Hi everyone, >> >> From FreeSurfer manual and discussion forum, I found that volume >> and LGI can be correlated using mri_glmfit command with -pvr flag. >> >> For that, my fsgd file has age, gender as covariates and the file >> is as following: >> >> GroupDescriptorFile 1 >> >> Class Male >> >> Class Female >> >> Variables Age >> >> Input zerek1 Male 21 >> >> Input zerek2 Male 25 >> >> etc. >> >> My concern is: >> >> To run mri_glmfit command, I am not sure how to define my >> contrast matrixif I am interested in removing the effect of age >> and sex. >> >> 1st option I tried is: 0 0.5 0.5 0 1 >> >> Here, I think first 0 regresses out age, 0.5 0.5 should be >> averaging over males and females and last 0 1 correlates between >> volume and LGI. But this looks like it is not giving me correct >> correlations maps, although there is no error. >> >> 2nd option I tried is: 0 0 0 0 1 >> >> This looks like its working and maps look correct to me >> but I want to make sure this is the correct contrast matrix and >> I am not sure how this matrix is regressing out age and gender or >> 1st option is correct contrast matrix? >> >> Thank you so much ! >> >> Best, >> >> Sahil >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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