can you send the design matrix Xg.mtx and the full terminal output?

On 08/08/2017 09:13 AM, Sullivan, Danielle Renee wrote:
>
> Hi FreeSurfer Experts,
>
>
> I am trying to run a dods cortical thickness analysis examining the 
> interaction of group on a continuous variable while controlling for 
> other variables.
>
>
> Specifically, I have 6 classes (gender by three groups [zero, one, 
> two]). I am interested in the group interaction with a continuous 
> variable while controlling for gender (among 4 other continuous 
> variables). I set up my fsgd file (see attached) and contrast file (36 
> dimensions- F test):
>
> *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 -1 0 1 
> -1 0]/2*
>
> *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 
> -1 1  0 -1]/2*
>
>
> and ran this command:
>
>
> *mri_glmfit --y 
> **lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh
>  
> --fsgd 
> fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
>  
> dods --C 
> /GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx 
> --surf fsaverage lh --cortex --glmdir 
> lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir
>  
> *
>
>
> But keep getting this error:
>
>
> *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08*
>
> *--------------------------------*
>
> *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.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh
>  
> --fsgd 
> fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
>  
> dods --C 
> /Volumes/VA_Imaging/Projects/salat/2389_TRT/dmiller/GGT_CRP/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx
>  
> --surf fsaverage lh --cortex --glmdir 
> lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir
>  
> *
>
> *  2. The FSGD file (if using one)*
>
> *  3. And the design matrix above*
>
>
>
> Any idea on what I am doing wrong?
>
>
> Danielle R. Miller, Ph.D.
>
> National Center for PTSD
>
> VA Boston Healthcare System Jamaica Plain
>
> Boston University School of Medicine
>
> OFFICE: (857) 364-4022
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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