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 <greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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