New subject: mri_glmfit ill-conditioned matrix question {Disarmed}

26 Oct 2019


      Hello,
I ran mri_glmfit with the following fsgd file:
GroupDescriptorFile 1			
Title CJD
Class MM1_MV1			
Class MV2_VV2
Variables	frontal
Input	7693	MV2_VV2	2.930667
Input	11985	MV2_VV2	2.410333
Input	13082	MV2_VV2	2.529333
Input	13425	MV2_VV2	2.593667
Input	13667	MM1_MV1	2.628667
Input	13900	MM1_MV1	2.675333
Input	14094	MM1_MV1	2.549333
Input	15566	MV2_VV2	2.666667
Input	15999	MM1_MV1	2.641
Input	16714	MV2_VV2	2.643
Input	16848	MV2_VV2	2.63
Input	16952	MV2_VV2	2.516
Input	7693a	MV2_VV2	3.054
Input	11985a	MV2_VV2	2.42
Input	13082a	MV2_VV2	2.454
Input	13425a	MV2_VV2	2.602
Input	13667a	MM1_MV1	2.604333
Input	13900a	MM1_MV1	2.601333
Input	14094a	MM1_MV1	2.523333
Input	15566a	MV2_VV2	2.713333
Input	15999a	MM1_MV1	2.584333
Input	16714a	MV2_VV2	2.673333
Input	16848a	MV2_VV2	2.533333
Input	16952a	MV2_VV2	2.486
My two contrast matrices are:
one.mtx = [ 0 0 1 0 ]
two.mtx = [ 0 0 0 1 ]
When running the mri_glmfit command "mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx”, I get the following output:
INFO: gd2mtx_method is dods
Saving design matrix to new.frontal.lgi/Xg.dat
Computing normalized matrix
Normalized matrix condition is 12820.7
Design matrix ------------------
 0.00000   1.00000   0.00000   2.93067;
 0.00000   1.00000   0.00000   2.41033;
 0.00000   1.00000   0.00000   2.52933;
 0.00000   1.00000   0.00000   2.59367;
 1.00000   0.00000   2.62867   0.00000;
 1.00000   0.00000   2.67533   0.00000;
 1.00000   0.00000   2.54933   0.00000;
 0.00000   1.00000   0.00000   2.66667;
 1.00000   0.00000   2.64100   0.00000;
 0.00000   1.00000   0.00000   2.64300;
 0.00000   1.00000   0.00000   2.63000;
 0.00000   1.00000   0.00000   2.51600;
 0.00000   1.00000   0.00000   3.05400;
 0.00000   1.00000   0.00000   2.42000;
 0.00000   1.00000   0.00000   2.45400;
 0.00000   1.00000   0.00000   2.60200;
 1.00000   0.00000   2.60433   0.00000;
 1.00000   0.00000   2.60133   0.00000;
 1.00000   0.00000   2.52333   0.00000;
 0.00000   1.00000   0.00000   2.71333;
 1.00000   0.00000   2.58433   0.00000;
 0.00000   1.00000   0.00000   2.67333;
 0.00000   1.00000   0.00000   2.53333;
 0.00000   1.00000   0.00000   2.48600;
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 12820.7
--------------------------------
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 --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx 
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further 
SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4)
 ... could not determine the cause of the problem
Can anyone give me some insight into what might be going wrong?
Thanks so much,
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
External Email - Use Caution