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 :* [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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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/ _______________________________________________ Freesurfer mailing list [email protected] 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.
