Hi, thanks for your reply, here is the output of the terminal in txt file, hope 
to hear from you soon
Merci
Hao
________________________________
De : [email protected] 
<[email protected]> de la part de Douglas Greve 
<[email protected]>
Envoyé : mercredi 1 juin 2016 17:06:19
À : [email protected]
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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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$
 ./AD_CN_COVARIATE_AGE_GENDER.sh
nsubjects = 60
tmpdir is ./tmp.mris_preproc.10192
/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
Log file is lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mris_preproc.log
Wed Jun  1 18:38:34 CEST 2016
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
cd 
/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
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/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

Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 
2014 x86_64 x86_64 x86_64 GNU/Linux
$Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
tmpdir is ./tmp.mris_preproc.10192
Src lh sphere.reg
Trg lh sphere.reg




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-----------------------
mri_concat 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0003/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//022_S_0007/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0010/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//067_S_0029/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0053/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//067_S_0076/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0083/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0084/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//123_S_0088/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//123_S_0091/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0093/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//123_S_0094/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//068_S_0109/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//067_S_0110/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//022_S_0129/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0139/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//032_S_0147/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//123_S_0162/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0183/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//136_S_0194/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//020_S_0213/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//005_S_0221/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//114_S_0228/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//128_S_0266/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//018_S_0286/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//136_S_0299/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//136_S_0300/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//128_S_0310/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//031_S_0321/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//035_S_0341/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0002/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0005/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0008/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//022_S_0014/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//100_S_0015/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0016/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//067_S_0019/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0021/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0022/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//011_S_0023/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0031/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//100_S_0035/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//099_S_0040/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//018_S_0043/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//100_S_0047/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//067_S_0056/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0058/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//067_S_0059/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0061/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//010_S_0067/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//007_S_0068/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//100_S_0069/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//007_S_0070/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//123_S_0072/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//027_S_0074/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//023_S_0081/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//136_S_0086/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//073_S_0089/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//099_S_0090/surf/lh.thickness.fwhm15.fsaverage.mgh
 
/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//032_S_0095/surf/lh.thickness.fwhm15.fsaverage.mgh
 --o lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh
ninputs = 60
Checking inputs
nframestot = 60
Allocing output
Done allocing
nframes = 60
Writing to lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh



Cleaning up
-----------------------
rm -r ./tmp.mris_preproc.10192
Wed Jun  1 18:38:36 CEST 2016
mris_preproc done
ERROR: must specify an input X file or fsgd file or --osgm
./AD_CN_COVARIATE_AGE_GENDER.sh: line 30: --y: command not found

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