Ok, sorry:
wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ mri_glmfit \
--glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir
ERROR: must specify an input X file or fsgd file or --osgm wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ --y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \
--C contrast.mtx \ --X X.mat
--y: command not found wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ --surf fsaverage lh \
--cortex \
Thanks
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N Greve greve@nmr.mgh.harvard.edu Envoyé : mercredi 1 juin 2016 18:47:19 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself
Can you send me just the terminal output from mri_glmfit?
On 06/01/2016 12:45 PM, Hao wen wrote:
Hi, thanks for your reply, here is the output of the terminal in txt file, hope to hear from you soon Merci Hao
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mercredi 1 juin 2016 17:06:19 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself 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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