that is quite strange. Does it happen every time? What is the mri_glmfit-sim command line and terminal output?
On 11/23/2022 2:47 PM, Vicente Ferrer wrote: > External Email - Use Caution > > Dear Freesurfer users, > > I was trying yo use mri_glmfit-sim after using mri_glmfit that run > successfully and I encounter this error: > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > -------------------------------- > -------- ERROR: READ THIS ----------------- > --vvvvvvvvvvvvvvvvvvvvvvvvvvvvvv----- > 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 --C > /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-29440/contrast_moca_groups.mtx > --sim perm 1000 1.5 > /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_b > br.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001 --sim-sign abs --fwhm 0 --fsgd > /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd > dods --mask /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg > 16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh --y > /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh > --perm-force --seed 1669778971 > 2. The terminal output of this program (ie, everything it prints to the > screen) > 3. The FSGD file > (/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd) > 4. The design matrix (null)/Xg.dat > Attempting to diagnose further > SumSq: Min=1.455099 (col 24), Max=8.657582 (col 23) > ... could not determine the cause of the problem > --^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^---- > > Seems like there is a problem with the condition matrix, but I do not > understand why. Could you help me with this problem? I attached the contrast > and fsgd files > > Best, > Vicente Ferrer > Predoctoral Researcher BCBL > http://secure-web.cisco.com/1kWZEOu8GTFhJvEwUHVoEpHYRwVtjwPjaW-68jFXGIsKvsccvtZ_SpRT4mbfMn9yTEj2SS5sODMuPyTAI7wxqhCmRxBRJ-35S_I8dxkyBkn-mSO5ejNKj3y_fRHlzfZYF0Y7e4avfl65oYvF1P9f6zlpO9fvp61CMx3UMDUkUt33HANwhKrNAQrsy2Y5VCcoRrA2AKBS0Z5P-jUa88tp7dylA1Zd2jmD5f7dpneDGC1UTgcKCSiQESkTtkx8M29TK78bxICiS2DYkMxYTENKlkex0JPgoayYX8JXmUgwvPcKnzKLxI-NITvFv7ql7vHrpEha80-krYMT5O5ictU2HZA/http%3A%2F%2Fwww.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: > http://secure-web.cisco.com/1rEQgkEB6hY4LJfH-np0OE9PS23Pj1ILuIHA5pV4sVGy6iIr-tPaz1dGNzeFeyqXXgVqPgUG9Qgp7lZdkhjdAcHDfLVn6s7EOi9wtR4KF_7pSBxwpwPdYFmAwjwozeIs_mTK37awik2WmWkYvzoV-QMyrLQrumy5vOdXlqgwK4yAk6dOtUj8cCE4shdj0ASydOPCuTVGQcNrMej809QxJJlq-1Q7gqxfnn3t8ouyZ19eLX1Q-lx0TFvoWRwwFe6tlQt7-xyz-DFdnxm9fdfvX6Oqx8jaubFX_2FfGKhpdxyfGxBbHvkSQ2U2P84Or7lYVraCUyjOe5ytoTdER0M4Zfg/http%3A%2F%2Fwww.bcbl.eu%2Flegal-disclaimer > > _______________________________________________ > 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
