please send the terminal output that includes the error
On 6/1/16 8:10 AM, Hao wen wrote:
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
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