Try demeaning and normalizing the covariates.
On 6/9/2021 9:09 AM, Lurie, Lucy wrote:
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Hello
I am trying to a whole brain analysis with one group and five
covariates. I am getting an error that the design matrix may be
ill-conditioned or badly scaled. I checked over the fsgd file in
TextEdit and it seems to be formatted correctly. I am using Freesurfer
version 5.3.0 and my platform is macOS Big Sur version 11.4. I would
appreciate any help further troubleshooting this error. Thank you!
ERROR: matrix is ill-conditioned or badly scaled, condno = 13065
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.eig_cgORCE_baselineORCE_teenCG.thickness.10.mgh --fsgd
eig_cgORCE_baselineORCE_teenCG.fsgd dods --C eig_cgORCE3042_slope.mtx
--C eig_cgORCEbaseline_slope.mtx --C eig_teenCGqual_slope.mtx --surf
fsaverage lh --cortex --glmdir
lh.eig_cgORCE_baselineORCE_teenCGagesex.glmdir
2. The FSGD file (if using one)
3. And the design matrix
Design matrix ------------------
1.000 0.000 16.660 2.950 2.200 0.000;
1.000 0.000 16.960 1.900 2.600 0.000;
1.000 0.000 17.390 2.450 2.800 0.000;
1.000 1.000 17.130 2.300 2.500 0.000;
1.000 1.000 16.980 2.400 2.300 0.000;
1.000 0.000 17.690 2.200 2.900 0.000;
1.000 1.000 16.870 2.750 2.900 1.000;
1.000 0.000 17.570 2.550 1.700 0.000;
1.000 0.000 17.130 2.150 1.928 0.000;
1.000 1.000 17.650 2.750 2.200 0.000;
1.000 1.000 17.210 2.450 2.500 1.000;
1.000 0.000 15.610 3.100 1.565 1.000;
1.000 0.000 16.440 2.650 2.300 0.000;
1.000 1.000 17.350 2.400 2.600 0.000;
1.000 0.000 16.800 1.600 1.400 0.000;
1.000 1.000 17.980 2.200 2.300 1.000;
1.000 1.000 16.890 2.800 1.600 1.000;
1.000 0.000 16.760 1.100 1.300 0.000;
1.000 1.000 16.790 2.500 1.400 0.000;
1.000 1.000 16.620 2.900 2.800 0.000;
1.000 1.000 16.500 2.500 1.200 0.000;
1.000 1.000 16.290 2.700 3.200 0.500;
1.000 0.000 16.440 3.100 2.500 1.000;
1.000 0.000 17.540 2.100 2.100 1.000;
1.000 1.000 16.810 1.900 2.600 1.000;
1.000 0.000 17.110 2.650 2.400 0.000;
1.000 1.000 16.520 2.000 2.300 0.000;
1.000 1.000 16.520 3.100 3.400 1.000;
1.000 0.000 16.320 3.300 2.800 0.500;
1.000 0.000 16.380 3.200 1.900 1.000;
1.000 0.000 16.570 2.800 2.000 0.000;
1.000 1.000 16.250 2.200 1.600 0.000;
1.000 1.000 16.820 2.900 2.600 1.000;
1.000 0.000 16.580 2.600 2.800 0.000;
1.000 1.000 16.730 2.850 3.150 0.000;
1.000 0.000 16.310 2.600 1.900 0.000;
1.000 1.000 17.010 1.700 2.400 0.000;
1.000 1.000 16.360 3.200 3.200 0.000;
1.000 1.000 16.490 2.400 1.525 0.000;
1.000 0.000 16.300 2.400 1.450 1.000;
1.000 0.000 16.060 2.200 1.300 0.000;
1.000 1.000 16.600 2.200 2.000 0.000;
1.000 0.000 16.720 3.300 2.500 0.000;
1.000 1.000 16.160 2.300 2.200 0.000;
1.000 1.000 16.140 2.800 1.850 0.000;
1.000 1.000 16.550 3.100 2.950 1.000;
1.000 1.000 17.300 3.450 2.700 1.000;
1.000 0.000 16.940 3.000 2.200 1.000;
1.000 1.000 16.550 2.700 2.850 0.000;
1.000 0.000 17.170 3.000 2.900 1.000;
1.000 0.000 17.150 2.800 2.450 0.000;
1.000 0.000 16.650 3.100 1.900 0.500;
1.000 0.000 16.070 2.700 2.900 1.000;
1.000 1.000 16.720 1.800 1.450 1.000;
1.000 0.000 16.150 2.900 1.000 0.000;
1.000 1.000 16.120 2.400 2.200 1.000;
1.000 1.000 17.540 2.600 2.600 0.000;
1.000 1.000 16.840 2.900 1.100 0.000;
1.000 1.000 15.790 3.100 1.600 1.000;
1.000 1.000 16.430 2.800 1.500 0.000;
1.000 0.000 16.390 3.300 2.700 1.000;
1.000 0.000 16.480 3.350 3.000 0.000;
1.000 1.000 16.930 3.000 1.000 0.000;
1.000 1.000 15.550 2.200 2.600 0.000;
1.000 1.000 17.080 2.900 1.500 0.000;
1.000 0.000 16.850 2.500 2.200 0.500;
1.000 1.000 16.700 2.200 1.800 0.000;
1.000 1.000 15.930 2.600 2.000 1.000;
1.000 1.000 16.080 2.600 1.200 0.500;
1.000 0.000 16.130 3.150 1.400 1.000;
1.000 1.000 16.250 3.100 1.400 1.000;
1.000 0.000 16.040 3.250 3.200 1.000;
1.000 0.000 16.040 3.500 2.900 1.000;
1.000 0.000 16.070 1.400 1.000 1.000;
1.000 0.000 16.550 3.200 2.300 1.000;
1.000 0.000 16.120 2.800 2.000 0.500;
1.000 1.000 16.450 3.150 1.400 1.000;
1.000 0.000 15.910 3.400 1.600 1.000;
1.000 1.000 15.700 3.000 2.400 1.000;
Best,
Lucy Lurie (she/her/hers)
Doctoral Student, Clinical Psychology
Department of Psychology and Neuroscience
University of North Carolina at Chapel Hill
CIRCLE Lab
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