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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Douglas N Greve <gr...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Douglas N Greve > <gr...@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-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Douglas Greve > > <gr...@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 > gr...@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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ > 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 gr...@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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
AD_CN_COVARIATES_AGE_GENDER.fsgd
Description: AD_CN_COVARIATES_AGE_GENDER.fsgd
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
