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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>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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