Hello, freesurfers:

I am doing group analysis, with two diff groups, so I want to know that how to create my own Contrast and Design matrix, because that I know in QDEC and CMline, in the freesurfer wiki, You just give the example for the DODS & DOSS, but it is not so flexible!

I know that we should define --X in the command mris_glmfit, but I got some problems, here is my work flow:

#set the SUBJECTS_DIR

export SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/

cd $SUBJECTS_DIR/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version

mris_preproc --fsgd AD_CN_COVARIATES_AGE_GENDER.fsgd \

--cache-in thickness.fwhm15.fsaverage \

--target fsaverage \

--hemi lh \

--out lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh

mri_glmfit \

--glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir

--y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \

--C AD_CN_COVARIATS_AGE_GENDER.mtx \

or --C contrast.mat

--X X.mat

--surf fsaverage lh \

--cortex \

so, after I run the mri_glmfit, i got the errors, like, you should define the --X or without --C, or cant find command --surf, --cortex, i dont really understand what is the problem, and I create the design matrix and contrast matrix in Matlab

Actually, I run the DODS, it works well, and the workflow, I dont change for the command mris_preproc, I just change the flags in mri_glmfit, someone could help me for this?

Thanks in advance!

Hao