Design matrix, not contrast matrix. It was printed out as part of the terminal output. It can also be found in glmdir/Xg.dat
On 05/26/2016 01:48 PM, Hanbyul Cho wrote: > Dear Douglas N Greve, > > The Contrast matrix was = [1 -1 0 0 0 0] > I attached the Xg.dat printed by unended mri_glmfit process. > > Thank you. > > Han. > > On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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> > <mailto: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> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto: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 > <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 > > > > > _______________________________________________ > 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
