Please send the design matrix On 05/24/2016 08:05 PM, Hanbyul Cho wrote: > Dear Douglas N Greve, > > Today, I tested the previous group analysis on other computer, and saw > the same error massage. > > I attached the tested fsgd and mtx files. > > command: > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd > 052416_PA_CO_G2V2.fsgd dods --glmdir > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage lh --C > 052416_contrast.mtx > > Thank you, > > Best wishes, > > Han > > > > > > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > If you seek help with this problem, make sure to send: > 1. Your command line: > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C > **G2V2.mtx --surf fsaverage lh --cortex --glmdir > lh.**G2V2.dods_sm15.glmdir > 2. The FSGD file (if using one) > 3. And the design matrix above > > On 05/21/2016 04:57 PM, Hanbyul Cho wrote: > > Dear FreeSurfer Team, > > > > I processed the Group analysis by FreeSurfer 5.3.0 > > > > Our data has two groups (Patient, Control) and two covariate values > > (age, extra value) > > mtx, contrast is 1 -1 0 0 0 0 > > The mris_preproc, and mri_surf2surf command were completed > without error. > > > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas > > thickness --out lh.**G2V2.dods.mgh > > mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh > --fwhm > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir > > lh.**G2V2.dods_sm15.glmdir > > > > After mri_glmfit command, I saw the error message. > > > > ========================================================= > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > -------------------------------- > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > If you seek help with this problem, make sure to send: > > 1. Your command line: > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir > > lh.**G2V2.dods_sm15.glmdir > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > ========================================================= > > > > I think our fsgd and mtx compositions are equal to the g2v2.fsgd > which > > FreeSurfer wiki example. > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V) > > > > In this situation, how can I correct my fsgd or mtx files? Is there > > any other command option? > > > > Best Regards, > > > > Han > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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 <mailto: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 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
