Hello-

I am trying to analyze the cortical thickness between two groups of
subjects Cl1 and CL2. When i run the GLM i receive the error:

matrix is ill-conditioned or badly scaled, condno = 1e+08

I am under the impression the error could be due to the non-uniformity in the range/scale of the regressors. 

here is my information:

contrast is 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0


1)  mri_glmfit --y lh.PvNPeverything.10.mgh --fsgd PvNPeverything.fsgd
dods --C PvNP_everything.mtx --surf UNM_ALLGOOD lh --cortex --glmdir
lh.PvNPeverything.glmdir

2) (sample of my fsgd) - there are no columns with all 0's in them
GroupDescriptorFile 1
Title Methedone Comparison
Class Cl1
Class Cl2
Variables  WAISIQ trait_anxiety alcohol_year heroin_year cocaine_year cannabis_year meth_year amphetamines_year meth_amphet_year hallucinogens_year   inhalants_year methodne_year opiates_year pills_year opitates_pills_year other_year total_years
Input M87160505 Cl1 86 33 10 3 9 11 0 1 1 1 8 0 0 6 6 0 49
Input M87161888 Cl1 109 59 0 0 7 22 0 0 0 0 0 0 0 0 0 0 32
Input M87107477 Cl1 89 34 12 0 9 13 0 9 9 6 10 0 1 9 10 0 57
Input M87199897 Cl1 117 44 0 23 0 10 0 0 0 0 0 9 15 0 15 3 60
Input M87146570 Cl1 94 42 26 0 3 8 0 0 0 0 0 0 0 0 0 6 37
Input M87189755 Cl1 111 59 11 0.5 2 15 0 3 3 1.5 0 0 0 0 0 0 36
Input M87169696 Cl1 86 22 2 0 11 14 0 0 0 0 0 0 0 0 0 0 25
Input M87187366 Cl1 106 51 28 0 27 0 0 20 20 0 0 0 0 0 0 0 75
Input M87178857 Cl2 117 48 0 4 4 8 0 5 5 7 0 4 0 0.08 0.08 0 42.08
Input M87165923 Cl2 103 40 5 2 0 15 0 0 0 0 0 0 0 1 1 0 23
Input M87110556 Cl2 134 60 4 0 1 15 0 0 0 0 0 0 0 0 0 0 20
Input M87183811 Cl2 97 43 15 0 8 3 0 0 0 0 0 0 0 0 0 0 26

3) design matrix

1 0 86 0 33 0 10 0 3 0 9 0 11 0 0 0 1 0 1 0 1 0 8 0 0 0 0 0 6 0 6 0 0 0 49 0
1 0 109 0 59 0 0 0 0 0 7 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0
1 0 89 0 34 0 12 0 0 0 9 0 13 0 0 0 9 0 9 0 6 0 10 0 0 0 1 0 9 0 10 0 0 0 57 0
1 0 89 0 40 0 15 0 5 0 2 0 30 0 10 0 0 0 10 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 59 0
1 0 77 0 44 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0
1 0 91 0 22 0 6 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0
1 0 103 0 29 0 20 0 3 0 11 0 27 0 0 0 11 0 11 0 5 0 0 0 0 0 0 0 1 0 1 0 0 0 78 0
1 0 117 0 44 0 0 0 23 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 9 0 15 0 0 0 15 0 3 0 60 0
1 0 94 0 42 0 26 0 0 0 3 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 37 0
1 0 91 0 38 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0
1 0 86 0 45 0 3 0 1 0 2 0 7 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 1 0 14 0
1 0 114 0 50 0 5 0 1 0 3 0 10 0 0 0 0.08 0 0.08 0 0 0 0 0 0.33 0 1 0 0 0 1 0 0 0 20.42 0
1 0 109 0 27 0 5 0 5 0 4 0 14 0 0 0 0 0 0 0 5 0 0 0 0 0 1 0 4 0 5 0 0 0 38 0
1 0 97 0 29 0 23 0 1 0 22 0 24 0 0 0 15 0 15 0 12 0 0 0 0 0 14 0 0 0 14 0 0 0 111 0
1 0 106 0 23 0 7 0 0 0 4 0 6 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0
1 0 131 0 25 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
1 0 74 0 54 0 12 0 0 0 0 0 16 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 6 0 6 0 0 0 32 0
1 0 123 0 41 0 0 0 0.17 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5.17 0
1 0 100 0 27 0 4 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0
1 0 111 0 59 0 11 0 0.5 0 2 0 15 0 0 0 3 0 3 0 1.5 0 0 0 0 0 0 0 0 0 0 0 0 0 36 0
1 0 86 0 22 0 2 0 0 0 11 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0
1 0 106 0 51 0 28 0 0 0 27 0 0 0 0 0 20 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 0
0 1 0 117 0 48 0 0 0 4 0 4 0 8 0 0 0 5 0 5 0 7 0 0 0 4 0 0 0 0.08 0 0.08 0 0 0 42.08
0 1 0 103 0 40 0 5 0 2 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 23
0 1 0 134 0 60 0 4 0 0 0 1 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20
0 1 0 97 0 43 0 15 0 0 0 8 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26
0 1 0 91 0 44 0 3 0 0 0 7 0 9 0 0 0 7 0 7 0 0 0 0 0 3 0 7 0 7 0 14 0 0 0 43
0 1 0 97 0 23 0 4.5 0 0 0 3 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27.5
0 1 0 72 0 48 0 3 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9
0 1 0 94 0 47 0 3.5 0 0 0 4 0 15.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23
0 1 0 100 0 45 0 0 0 0 0 0 0 2 0 0 0 0.5 0 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6.5
0 1 0 100 0 36 0 15 0 0 0 0 0 10 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 28
0 1 0 94 0 45 0 0 0 15 0 0 0 20 0 0 0 0 0 0 0 0 0 0.5 0 0 0 0 0 0 0 0 0 5 0 50.5
0 1 0 103 0 58 0 11 0 2 0 6 0 6 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 35
0 1 0 83 0 31 0 22 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0.5 0 0 0 0 0 0 0 0 0 0 0 35.5
0 1 0 91 0 54 0 10 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25
0 1 0 97 0 38 0 5 0 0 0 1 0 7 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 14
0 1 0 72 0 34 0 9 0 0 0 0 0 9 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12
0 1 0 80 0 44 0 1 0 0 0 1 0 4 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7
0 1 0 114 0 54 0 14 0 0 0 0 0 14 0 0 0 14 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38
0 1 0 89 0 33 0 9 0 17 0 17 0 9 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 49
0 1 0 89 0 60 0 0 0 0 0 10 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26
0 1 0 72 0 42 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2
0 1 0 89 0 34 0 1 0 0 0 0 0 5 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8
0 1 0 94 0 53 0 5 0 0 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15
0 1 0 91 0 25 0 15 0 0 0 23 0 31 0 3 0 0 0 3 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 82
0 1 0 91 0 36 0 8 0 0 0 0 0 19 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 33
0 1 0 100 0 53 0 20 0 0 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19
0 1 0 91 0 42 0 20 0 0 0 15 0 15 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45
0 1 0 91 0 52 0 8 0 0 0 0 0 10 0 0 0 4 0 4 0 2 0 0 0 0 0 1 0 0 0 1 0 0 0 18
0 1 0 74 0 36 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3
0 1 0 91 0 43 0 2 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13
0 1 0 91 0 24 0 1 0 0 0 1 0 14 0 0 0 12 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 29
0 1 0 109 0 24 0 13 0 0 0 3 0 3 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 27
0 1 0 117 0 39 0 21 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 6
0 1 0 126 0 40 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 0 77 0 50 0 5 0 0.17 0 0 0 6 0 0 0 0 0 0 0 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 11.42
0 1 0 86 0 37 0 7 0 3 0 1 0 7 0 0 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23
0 1 0 91 0 40 0 12 0 0 0 0 0 12 0 8 0 0 0 8 0 0 0 0 0 0 0 0.5 0 0 0 0.5 0 0 0 32.5
0 1 0 97 0 42 0 1.5 0 0 0 2 0 6 0 4 0 0 0 4 0 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 14
0 1 0 91 0 37 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12
0 1 0 91 0 48 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 4.25
0 1 0 94 0 58 0 1 0 0 0 0.67 0 4 0 5 0 0 0 5 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 13.67
0 1 0 114 0 48 0 17 0 0 0 6 0 17 0 0 0 7 0 7 0 5 0 0 0 0 0 0 0 2 0 2 0 0 0 50
0 1 0 106 0 54 0 15 0 0 0 7 0 15 0 0 0 15 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44
0 1 0 74 0 46 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5
0 1 0 91 0 43 0 0 0 0 0 0 0 0 0 0 0 0.33 0 0.33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33
0 1 0 80 0 27 0 3 0 30 0 0 0 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60
0 1 0 97 0 33 0 0.5 0 0 0 0.25 0 2 0 2 0 0 0 2 0 0 0 0.17 0 0 0 0 0 0 0 0 0 0 0 4.92
0 1 0 100 0 31 0 6 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9
0 1 0 109 0 29 0 0 0 0 0 0 0 13 0 0 0 10 0 10 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 24
0 1 0 80 0 37 0 0 0 0 0 8 0 8 0 0.5 0 0 0 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16.5
0 1 0 72 0 55 0 10 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20
0 1 0 103 0 40 0 0 0 0.5 0 1 0 8 0 0.67 0 0 0 0.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10.17
0 1 0 77 0 32 0 0 0 0.5 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12.5
0 1 0 120 0 28 0 0 0 0 0 4 0 12 0 0 0 7 0 7 0 4 0 0 0 0 0 0 0 0 0 0 0 7 0 34
0 1 0 86 0 32 0 11 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19
0 1 0 91 0 44 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3
0 1 0 94 0 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 0 100 0 29 0 5 0 0 0 0 0 16 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38
0 1 0 94 0 25 0 4 0 0 0 0.5 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12.5
0 1 0 74 0 51 0 10 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30
0 1 0 97 0 36 0 30 0 0 0 20 0 33 0 5 0 6 0 11 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 90
0 1 0 117 0 35 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5
0 1 0 80 0 51 0 7 0 4 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19
0 1 0 103 0 28 0 9 0 0 0 1 0 1 0 0 0 8 0 8 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 27
0 1 0 103 0 74 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6
0 1 0 89 0 57 0 10 0 0 0 0 0 0 0 15 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18
0 1 0 109 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 0 109 0 28 0 3 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5
0 1 0 91 0 27 0 20 0 0 0 15 0 0 0 3 0 0 0 3 0 0 0 0 0 0 0 17 0 0 0 17 0 0 0 55
0 1 0 89 0 48 0 9 0 0 0 0.25 0 10 0 20 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39.25
0 1 0 97 0 28 0 10 0 0 0 4 0 10 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29
0 1 0 100 0 40 0 3 0 0 0 0 0 0.17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3.17
0 1 0 89 0 21 0 20 0 8 0 25 0 25 0 10 0 0 0 10 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 90
0 1 0 103 0 54 0 10 0 0 0 2 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12
0 1 0 77 0 49 0 0 0 0 0 10 0 12 0 0 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 42
0 1 0 89 0 42 0 0 0 0 0 4 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14
0 1 0 117 0 34 0 25 0 0 0 2 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52
0 1 0 83 0 56 0 12 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15
0 1 0 91 0 33 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2
0 1 0 106 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 0 120 0 50 0 1 0 0 0 0 0 2 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6

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Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign 
BA - Psych - University of Wisconsin-Madison
mdkruepke@gmail.com
(262)-483-7449