bash-3.2$ mri_glmfit --y results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh --fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf fsaverage lh --cortex --glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir gdfRead(): reading thickness_DHI_Emotional_edit.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 47.0476 9.22459 1 Sports 0.619048 1.13289 2 Days_TBI 1734.1 919.571 3 Emotional 13.5238 7.19536 Class Size and Means of each Continuous Variable 1 PPCS_male 5 39.8000 1.6000 1557.8000 12.8000 2 PPCS_female 16 49.3125 0.3125 1789.1875 13.7500 WARNING: Class PPCS_male has 5 members. With 4 variables and using DODS, This is the bare minimum which may cause problems with the design matrix. INFO: gd2mtx_method is dods Reading source surface /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.2.0 cwd /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness cmdline mri_glmfit --y results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh --fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf fsaverage lh --cortex --glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir sysname Darwin hostname ip-130-63-40-126.dynamic.yorku.ca machine x86_64 user sergiolab FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh logyflag 0 usedti 0 FSGD thickness_DHI_Emotional_edit.fsgd labelmask /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/label/lh.cortex.label maskinv 0 glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir Loading y from /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 653034 Design matrix ------------------ 1.00000 0.00000 30.00000 0.00000 4.00000 0.00000 1687.00000 0.00000 10.00000 0.00000; 0.00000 1.00000 0.00000 46.00000 0.00000 0.00000 0.00000 2149.00000 0.00000 12.00000; 1.00000 0.00000 41.00000 0.00000 0.00000 0.00000 2148.00000 0.00000 6.00000 0.00000; 0.00000 1.00000 0.00000 49.00000 0.00000 0.00000 0.00000 2257.00000 0.00000 18.00000; 0.00000 1.00000 0.00000 51.00000 0.00000 0.00000 0.00000 1939.00000 0.00000 28.00000; 0.00000 1.00000 0.00000 61.00000 0.00000 0.00000 0.00000 3404.00000 0.00000 8.00000; 0.00000 1.00000 0.00000 53.00000 0.00000 0.00000 0.00000 2368.95825 0.00000 6.00000; 0.00000 1.00000 0.00000 60.00000 0.00000 2.00000 0.00000 1407.00000 0.00000 10.00000; 0.00000 1.00000 0.00000 48.00000 0.00000 0.00000 0.00000 1670.95837 0.00000 6.00000; 0.00000 1.00000 0.00000 38.00000 0.00000 0.00000 0.00000 12.00000 0.00000 26.00000; 0.00000 1.00000 0.00000 63.00000 0.00000 0.00000 0.00000 796.00000 0.00000 18.00000; 0.00000 1.00000 0.00000 40.00000 0.00000 0.00000 0.00000 476.00000 0.00000 6.00000; 0.00000 1.00000 0.00000 44.00000 0.00000 2.00000 0.00000 1980.00000 0.00000 14.00000; 0.00000 1.00000 0.00000 50.00000 0.00000 1.00000 0.00000 3517.04175 0.00000 6.00000; 1.00000 0.00000 29.00000 0.00000 1.00000 0.00000 177.04167 0.00000 18.00000 0.00000; 0.00000 1.00000 0.00000 39.00000 0.00000 0.00000 0.00000 2571.00000 0.00000 22.00000; 0.00000 1.00000 0.00000 53.00000 0.00000 0.00000 0.00000 1872.00000 0.00000 18.00000; 1.00000 0.00000 59.00000 0.00000 0.00000 0.00000 1148.00000 0.00000 24.00000 0.00000; 0.00000 1.00000 0.00000 50.00000 0.00000 0.00000 0.00000 1250.04163 0.00000 16.00000; 1.00000 0.00000 40.00000 0.00000 3.00000 0.00000 2628.95825 0.00000 6.00000 0.00000; 0.00000 1.00000 0.00000 44.00000 0.00000 0.00000 0.00000 957.00000 0.00000 6.00000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 653034 -------------------------------- -------- 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 --y results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh --fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf fsaverage lh --cortex --glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir 2. The terminal output of this program (ie, everything it prints to the screen) 3. The FSGD file (thickness_DHI_Emotional_edit.fsgd) 4. The design matrix results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir/Xg.dat Attempting to diagnose further WARNING: Class PPCS_male has 5 members. With 4 variables and using DODS, This is the bare minimum which may cause problems with the design matrix. SumSq: Min=2.236068 (col 1), Max=8073.791016 (col 8) The scale is much different between columns 1 and 8, you may want to normalize by subtracting the mean and dividing by the standard deviation. --^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^---- bash-3.2$