Dear FreeSurfer Team, I wonder you could not read an previous attached file.
Thank you, Han On Thu, May 26, 2016 at 12:12 PM, Hanbyul Cho <hanbyul.h....@gmail.com> wrote: > Dear Douglas N Greve, > > > I sent again this design matrix (= Xg.dat) by attached. > > Thank you. > > Han. > > On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> 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 >> > >
_______________________________________________ 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.
