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