Hi Freesurfer Experts,
I am trying to run mri_glmfit and while 90% of my files work, some of them display the error below. I have tried demeaning, and then tried multiplying this value by 100, and I still get the same error. Any feedback would be greatly appreciated.
mris_preproc done srcsubject = fsaverage srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh srctype = trgsubject = fsaverage trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh gdfReadHeader: reading /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 19.5833 1.32025 1 eTIV 1.61645e+06 145343 2 EnglishParityRT 0.00012207 25139.1 Class Means of each Continuous Variable 1 Monolingual_male 19.7143 1678946.5893 -4197.2796 2 Monolingual_female 19.4000 1528966.6750 5876.1917 INFO: gd2mtx_method is dods Reading source surface /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /gpfs/scratch/jtl190/Math_reconstruction cmdline mri_glmfit --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd --C /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir sysname Linux hostname cyberstar129.hpc.rcc.psu.edu machine x86_64 user jtl190 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh logyflag 0 usedti 0 FSGD /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd labelmask /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir Loading y from /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat Normalized matrix condition is 22568.9 Design matrix ------------------ 1.000 0.000 18.000 0.000 1865790.250 0.000 -8952.208 0.000; 0.000 1.000 0.000 19.000 0.000 1520429.625 0.000 -4605.208; 1.000 0.000 19.000 0.000 1749716.750 0.000 -39407.207 0.000; 0.000 1.000 0.000 18.000 0.000 1589109.250 0.000 -17967.209; 1.000 0.000 21.000 0.000 1472295.125 0.000 19531.791 0.000; 1.000 0.000 18.000 0.000 1580381.375 0.000 -17027.209 0.000; 1.000 0.000 20.000 0.000 1813373.500 0.000 16152.792 0.000; 1.000 0.000 21.000 0.000 1638616.500 0.000 -9074.208 0.000; 0.000 1.000 0.000 21.000 0.000 1297920.500 0.000 61860.793; 0.000 1.000 0.000 18.000 0.000 1634762.625 0.000 -22671.209; 0.000 1.000 0.000 21.000 0.000 1602611.375 0.000 12763.792; 1.000 0.000 21.000 0.000 1632452.625 0.000 9395.292 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9 -------------------------------- 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 rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd --C /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir 2. The FSGD file (if using one) 3. And the design matrix above
I am also attaching the FSGD file.
Best,
Jennifer Legault