Hi, so i changed my design matrix, let the gender*group(AD,Contrrol), so this time the design matrix is like this, which i think it is ok
AgeSubjects Female*AD Male*AD Female*Control Male*Control
+74.30000 +0.00000 +0.00000 +0.00000 +1.00000 +73.70000 +0.00000 +0.00000 +0.00000 +1.00000 +84.50000 +0.00000 +0.00000 +1.00000 +0.00000 +78.50000 +0.00000 +0.00000 +1.00000 +0.00000 +80.80000 +0.00000 +0.00000 +0.00000 +1.00000 +65.40000 +0.00000 +0.00000 +0.00000 +1.00000 +73.10000 +0.00000 +0.00000 +1.00000 +0.00000 +72.60000 +0.00000 +0.00000 +1.00000 +0.00000 +63.20000 +0.00000 +0.00000 +0.00000 +1.00000 +71.70000 +0.00000 +0.00000 +0.00000 +1.00000 +77.70000 +0.00000 +0.00000 +1.00000 +0.00000 +76.90000 +0.00000 +0.00000 +0.00000 +1.00000 +73.20000 +0.00000 +0.00000 +0.00000 +1.00000 +76.20000 +0.00000 +0.00000 +0.00000 +1.00000 +84.70000 +0.00000 +0.00000 +0.00000 +1.00000 +69.60000 +0.00000 +0.00000 +1.00000 +0.00000 +70.10000 +0.00000 +0.00000 +0.00000 +1.00000 +70.90000 +0.00000 +0.00000 +1.00000 +0.00000 +77.00000 +0.00000 +0.00000 +1.00000 +0.00000 +74.50000 +0.00000 +0.00000 +0.00000 +1.00000 +74.40000 +0.00000 +0.00000 +1.00000 +0.00000 +72.90000 +0.00000 +0.00000 +0.00000 +1.00000 +74.00000 +0.00000 +0.00000 +0.00000 +1.00000 +70.60000 +0.00000 +0.00000 +0.00000 +1.00000 +78.20000 +0.00000 +0.00000 +0.00000 +1.00000 +70.60000 +0.00000 +0.00000 +0.00000 +1.00000 +80.30000 +0.00000 +0.00000 +1.00000 +0.00000 +65.10000 +0.00000 +0.00000 +0.00000 +1.00000 +69.80000 +0.00000 +0.00000 +0.00000 +1.00000 +71.10000 +0.00000 +0.00000 +0.00000 +1.00000 +81.30000 +0.00000 +1.00000 +0.00000 +0.00000 +75.40000 +0.00000 +1.00000 +0.00000 +0.00000 +73.90000 +1.00000 +0.00000 +0.00000 +0.00000 +64.10000 +0.00000 +1.00000 +0.00000 +0.00000 +80.10000 +0.00000 +1.00000 +0.00000 +0.00000 +78.30000 +0.00000 +1.00000 +0.00000 +0.00000 +73.20000 +0.00000 +1.00000 +0.00000 +0.00000 +75.30000 +1.00000 +0.00000 +0.00000 +0.00000 +65.60000 +0.00000 +1.00000 +0.00000 +0.00000 +62.40000 +0.00000 +1.00000 +0.00000 +0.00000 +77.20000 +1.00000 +0.00000 +0.00000 +0.00000 +70.70000 +1.00000 +0.00000 +0.00000 +0.00000 +70.10000 +1.00000 +0.00000 +0.00000 +0.00000 +82.60000 +1.00000 +0.00000 +0.00000 +0.00000 +80.20000 +1.00000 +0.00000 +0.00000 +0.00000 +65.90000 +1.00000 +0.00000 +0.00000 +0.00000 +59.70000 +1.00000 +0.00000 +0.00000 +0.00000 +71.80000 +0.00000 +1.00000 +0.00000 +0.00000 +72.40000 +1.00000 +0.00000 +0.00000 +0.00000 +80.50000 +1.00000 +0.00000 +0.00000 +0.00000 +62.90000 +0.00000 +1.00000 +0.00000 +0.00000 +67.40000 +0.00000 +1.00000 +0.00000 +0.00000 +80.20000 +1.00000 +0.00000 +0.00000 +0.00000 +85.50000 +0.00000 +1.00000 +0.00000 +0.00000 +65.90000 +0.00000 +1.00000 +0.00000 +0.00000 +89.10000 +1.00000 +0.00000 +0.00000 +0.00000 +56.40000 +0.00000 +1.00000 +0.00000 +0.00000 +82.70000 +0.00000 +1.00000 +0.00000 +0.00000 +68.30000 +0.00000 +1.00000 +0.00000 +0.00000 +74.00000 +0.00000 +1.00000 +0.00000 +0.00000
But when i design the Contrast.mat, I got some error,
ERROR: loading C Contrast_5_intersect.mat
I defined my contrast like this:
0 1 1 -1 -1
or
1 0 1 1 -1 -1
or
0 1 1 -1 -1 0
neither of them work..
Thank you for your patience:)
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mercredi 8 juin 2016 10:19:02 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself
Also, as far as I know, in Surfstat, we can treat the categorized factor as the covirates, but in FS, the categorized factor should be treated as a class? is that because of this?
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mercredi 8 juin 2016 10:10:52 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself
Ok, So in FS, you can not define your design matrix like this? cuz in Surfstat, i can define the design matrix like this, the five columns represent AD, Control, Age, female and male, because in FS, I know we can do the DODS & DOSS, but I want to design some more flexible design matrix, and for the Contrast wiht .mat file, what do you mean:
--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.
Hope to hear from you soon:)
________________________________ 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 : mardi 7 juin 2016 16:39:45 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself
Columns (1+2) = Columns (4+5) in the desgin matrix. This causes the error
On 6/7/16 5:56 AM, Hao wen wrote:
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Envoyé : lundi 6 juin 2016 17:47:15 À : freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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$mailto:wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ 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$mailto:wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ --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$mailto:wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ --surf fsaverage lh \
--cortex \
Thanks
*De :* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Envoyé :* mercredi 1 juin 2016 18:47:19 *À :* freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Envoyé :* mercredi 1 juin 2016 17:06:19 *À :* freesurfer@nmr.mgh.harvard.edumailto: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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