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%22> Wed, 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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