1) Sorry, I don't understand what you are trying to do

2) Depends on what you are testing. If you are looking at the slopes of the covariates, then demeaning is not important. If you are looking at group differences, you should first look for a difference in the slopes. If there is no significant differences, then reanalyze using DOSS instead of DODS in which case demeaning will not matter.

3) Correct

On 09/29/2016 09:09 AM, Damien MARIE wrote:

Hi,

Many thanks for your prompt reply Pr. Greve.

I did :

mri_glmfit --y /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh --fsgd /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA --surf fsaverage rh --label /home/damien/bin/freesurfer/subjects/fsaverage/label/rh.aparc.label --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Avg-Intercept-area.mat --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-dyslexic-control-Intercept-area.mat --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-male-female-Intercept-area.mat --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-X-group-gender-Intercept-area.mat --eres-save

mri_segstats --in /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/eres.mgh --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf RH_Dys-CT_CSA_AgeGenderWRCSA.dat

1. I don’t get it though. Probably I made a bad description of my

goal, perhaps using this terminology of “residuals” also is not very accurate.

I exported the txt file (output of mri_segstats computed on eres.mgh) to a statistical software and ran a mancova per cluster on cluster values with covariatess : age, right hemispheric surface area + gender factor. I find significant effects of the covariates on 7/9 clusters.

I was not expecting such effects. I wanted to extract residuals of surface area in the significant clusters obtain using the Qdec Monte Carlo simulation on the contrast of interest (Dys - Ct) after removing all covariate effects.

My aim was to look at the differences between the two levels of the factor of interest to get a sense of what is happening in this Qdec analysis and this particular contrast of interest. These results are in an opposite direction in comparison with other Qdec analysis without covariates / ROI analysis on surface area residuals after removing effect of gender, age and right hemispheric surface area (Destrieux's labels) / Whole-brain VBM analyses with covariates (not on surface area then...)

Basically I have the feeling there is something wrong with the contrast display in this particular qdec analysis. I don’t know how I could get what I called the CSA residuals in the framework of this analysis.

2. Another question: should I standardize or center my covariates

before proceeding to the analysis?

3. A silly question probably but to be 100% sure… If in the

qdec.table.dat, order of subjects is first group “ dys “ then second group “ ct “ and that the contrast is called: rh-Diff-dys-dyslexic-control-intercept-area , negative p value means decrease of surface area in the first group (dys) as compared to the second group (ct), right ?

Thank you and best, *Damien MARIE*

*Douglas Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22Wed, 28 Sep 2016 12:40:51 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160928*

*Those are not residuals. If you want residuals, you will need to run mri_glmfit from the command line adding --eres-save. You can get the command line from the mri_glmfit.log file in the glmdir*

On 9/28/16 10:58 AM, Damien MARIE wrote:

Dear FreeSurfers,

Sorry for the repost. I’m still trying to extract the residuals of
cortical surface area from a qdec analysis with two factors (2
levels) and 2 covariates.

I tried this command line:

mri_segstats --in
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh
--sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf
RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9
columns (number of clusters) and 69 lines (number of subjects).
Now I am not 100% sure it’s really the residuals (y.mgh) so I
would be glad if somebody could tell me please.

Best,
Damien
Original post:
Dear experts,

I would like to know what is the best and simplest way to extract cortical
surface area and thickness from clusters obtained after a Monte Carlo
correction. This is a group comparison I did with qdec including gender as
discrete variable + age and mean thickness or whole hemispheric surface area as
nuisance factors, so I would like to get the feature residuals after the
removal of the covariate effects.
I am sorry, I saw several posts about that but for me it’s not completely clear
what command line I should use to get tables for this…

Thank you and best,
Damien




*Damien MARIE*

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