Hello:

Also, for the contrast matrix, I am a little confused about the explaination in FS wiki:

--C contrast1.mat <--C contrast2.mat ...>

Specify one or more contrasts to test. The contrast.mat file is an ASCII text file with the contrast matrix in it (make sure the last line is blank). The output will be saved in glmdir/contrast1, glmdir/contrast2, etc. Eg, if --C norm-v-cont.mat, then the ouput will be glmdir/norm-v-cont.


what does the (make sure the last line is blank) mean? 


when I changed the dimension for the design matrix, it gave me some errors like :


ERROR: loading C contrast.mat

I change the .mat file to .mtx(add 1 in the first column) file for the contrast, it worked,  but in the subdirecotry in the contrast, the contrast in c.dat file seems to be wrong, not what I excepted:)
 
Hope to hear from you soon.

De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Hao wen <hao.freesurfer@hotmail.com>
Envoyé : mardi 7 juin 2016 11:56:51
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself
 

Thanks, Doug:

That was a really silly mistake, so right now I can run the cmdline for mri_glmfit

but I got the error like this:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07
--------------------------------
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

1,here is my cmdline:


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 contrast.mat \
  --X X.mat\
  --surf fsaverage lh \
  --cortex \

So after this, I got my design matrix as below:

+0.00000 +1.00000 +74.30000 +0.00000 +1.00000 
+0.00000 +1.00000 +73.70000 +0.00000 +1.00000 
+0.00000 +1.00000 +84.50000 +1.00000 +0.00000 
+0.00000 +1.00000 +78.50000 +1.00000 +0.00000 
+0.00000 +1.00000 +80.80000 +0.00000 +1.00000 
+0.00000 +1.00000 +65.40000 +0.00000 +1.00000 
+0.00000 +1.00000 +73.10000 +1.00000 +0.00000 
+0.00000 +1.00000 +72.60000 +1.00000 +0.00000 
+0.00000 +1.00000 +63.20000 +0.00000 +1.00000 
+0.00000 +1.00000 +71.70000 +0.00000 +1.00000 
+0.00000 +1.00000 +77.70000 +1.00000 +0.00000 
+0.00000 +1.00000 +76.90000 +0.00000 +1.00000 
+0.00000 +1.00000 +73.20000 +0.00000 +1.00000 
+0.00000 +1.00000 +76.20000 +0.00000 +1.00000 
+0.00000 +1.00000 +84.70000 +0.00000 +1.00000 
+0.00000 +1.00000 +69.60000 +1.00000 +0.00000 
+0.00000 +1.00000 +70.10000 +0.00000 +1.00000 
+0.00000 +1.00000 +70.90000 +1.00000 +0.00000 
+0.00000 +1.00000 +77.00000 +1.00000 +0.00000 
+0.00000 +1.00000 +74.50000 +0.00000 +1.00000 
+0.00000 +1.00000 +74.40000 +1.00000 +0.00000 
+0.00000 +1.00000 +72.90000 +0.00000 +1.00000 
+0.00000 +1.00000 +74.00000 +0.00000 +1.00000 
+0.00000 +1.00000 +70.60000 +0.00000 +1.00000 
+0.00000 +1.00000 +78.20000 +0.00000 +1.00000 
+0.00000 +1.00000 +70.60000 +0.00000 +1.00000 
+0.00000 +1.00000 +80.30000 +1.00000 +0.00000 
+0.00000 +1.00000 +65.10000 +0.00000 +1.00000 
+0.00000 +1.00000 +69.80000 +0.00000 +1.00000 
+0.00000 +1.00000 +71.10000 +0.00000 +1.00000 
+1.00000 +0.00000 +81.30000 +0.00000 +1.00000 
+1.00000 +0.00000 +75.40000 +0.00000 +1.00000 
+1.00000 +0.00000 +73.90000 +1.00000 +0.00000 
+1.00000 +0.00000 +64.10000 +0.00000 +1.00000 
+1.00000 +0.00000 +80.10000 +0.00000 +1.00000 
+1.00000 +0.00000 +78.30000 +0.00000 +1.00000 
+1.00000 +0.00000 +73.20000 +0.00000 +1.00000 
+1.00000 +0.00000 +75.30000 +1.00000 +0.00000 
+1.00000 +0.00000 +65.60000 +0.00000 +1.00000 
+1.00000 +0.00000 +62.40000 +0.00000 +1.00000 
+1.00000 +0.00000 +77.20000 +1.00000 +0.00000 
+1.00000 +0.00000 +70.70000 +1.00000 +0.00000 
+1.00000 +0.00000 +70.10000 +1.00000 +0.00000 
+1.00000 +0.00000 +82.60000 +1.00000 +0.00000 
+1.00000 +0.00000 +80.20000 +1.00000 +0.00000 
+1.00000 +0.00000 +65.90000 +1.00000 +0.00000 
+1.00000 +0.00000 +59.70000 +1.00000 +0.00000 
+1.00000 +0.00000 +71.80000 +0.00000 +1.00000 
+1.00000 +0.00000 +72.40000 +1.00000 +0.00000 
+1.00000 +0.00000 +80.50000 +1.00000 +0.00000 
+1.00000 +0.00000 +62.90000 +0.00000 +1.00000 
+1.00000 +0.00000 +67.40000 +0.00000 +1.00000 
+1.00000 +0.00000 +80.20000 +1.00000 +0.00000 
+1.00000 +0.00000 +85.50000 +0.00000 +1.00000 
+1.00000 +0.00000 +65.90000 +0.00000 +1.00000 
+1.00000 +0.00000 +89.10000 +1.00000 +0.00000 
+1.00000 +0.00000 +56.40000 +0.00000 +1.00000 
+1.00000 +0.00000 +82.70000 +0.00000 +1.00000 
+1.00000 +0.00000 +68.30000 +0.00000 +1.00000 
+1.00000 +0.00000 +74.00000 +0.00000 +1.00000 

My contrast matix, contrast.mat is like this: the first and second columns are Control and AD

1 -1 0 0 0 

in the mris_preproc command, i used the fsgd file, so ill also attach it to you!

Thanks in advance!
Hao


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 : lundi 6 juin 2016 17:47:15
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself
 
looks like you put your command on two different lines

On 06/06/2016 05:16 AM, Hao wen wrote:
> Sorry, if you received my email, cuz I really stucked here, and i
> didnt find the related topics in the freesurfer support archive!
> Thank you in advance
> ------------------------------------------------------------------------
> *De :* Hao wen
> *Envoyé :* mercredi 1 juin 2016 19:32:24
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* RE: [Freesurfer] CM_Group_analysis_Create tha contrast and
> design matrix by myself
> 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
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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