My guess is that your covariates have almost no range to them and so look like constant (similar to columns 1 and 2). You can try demeaning and rescaling the covariates. You can do this by hand and create a new FSGD file or you can add the following lines anywhere in the fsgd: RescaleFlag 1 DemeanFlag 1
On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote: 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer