Hi Daniel, please remember to post to the list instead of me directly ... to answer your question, this is probably just a matter of scaling. Try removing the mean and dividing by the standard deviation of the linear, quad, and cubic. More recent versions of FS should do this automatically.
doug
On 09/25/2013 06:01 AM, Daniel Klein wrote:
Hi Doug,
thanks a lot. I want to use qdec for this pupose.
When i add Age (cubic) as continous factor and age as nuisance factor in the model it works fine.
In the model age (square) as continous factor and age as nuisance i get the following error:
Creating output directory /Users/dolphinede/Desktop/Probanden/qdec/Untitled Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat Normalized matrix condition is 22042.4 Design matrix ------------------ 1.000 169.000 13.000; 1.000 225.000 15.000; 1.000 225.000 15.000; 1.000 256.000 16.000; 1.000 225.000 15.000; 1.000 400.000 20.000; 1.000 196.000 14.000; 1.000 256.000 16.000; 1.000 144.000 12.000; 1.000 169.000 13.000; 1.000 361.000 19.000; 1.000 289.000 17.000; 1.000 289.000 17.000; 1.000 196.000 14.000; 1.000 361.000 19.000; 1.000 196.000 14.000; 1.000 169.000 13.000; 1.000 324.000 18.000; 1.000 225.000 15.000; 1.000 225.000 15.000; 1.000 324.000 18.000; 1.000 529.000 23.000; 1.000 400.000 20.000; 1.000 484.000 22.000; 1.000 529.000 23.000; 1.000 324.000 18.000; 1.000 484.000 22.000; 1.000 324.000 18.000; 1.000 256.000 16.000; 1.000 361.000 19.000; 1.000 256.000 16.000; 1.000 289.000 17.000; 1.000 289.000 17.000; 1.000 256.000 16.000; 1.000 256.000 16.000; 1.000 441.000 21.000; 1.000 289.000 17.000; 1.000 289.000 17.000; 1.000 225.000 15.000; 1.000 256.000 16.000; 1.000 225.000 15.000; 1.000 225.000 15.000; 1.000 400.000 20.000; 1.000 289.000 17.000; 1.000 324.000 18.000; 1.000 256.000 16.000; 1.000 484.000 22.000; 1.000 361.000 19.000; 1.000 256.000 16.000; 1.000 529.000 23.000; 1.000 400.000 20.000; 1.000 484.000 22.000; 1.000 441.000 21.000; 1.000 324.000 18.000; 1.000 361.000 19.000; 1.000 484.000 22.000; 1.000 361.000 19.000; 1.000 441.000 21.000; 1.000 324.000 18.000; 1.000 144.000 12.000; 1.000 361.000 19.000; 1.000 441.000 21.000; 1.000 441.000 21.000; 1.000 441.000 21.000; 1.000 529.000 23.000; 1.000 324.000 18.000; 1.000 361.000 19.000; 1.000 289.000 17.000; 1.000 529.000 23.000; 1.000 484.000 22.000; 1.000 441.000 21.000; 1.000 196.000 14.000; 1.000 169.000 13.000; 1.000 196.000 14.000; 1.000 361.000 19.000; 1.000 196.000 14.000; 1.000 169.000 13.000; 1.000 400.000 20.000;
1.000 361.000 19.000;
ERROR: matrix is ill-conditioned or badly scaled, condno = 22042.4
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:
- Your command line:
mri_glmfit --y/Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh --fsgd /Users/dolphinede/Desktop/Probanden/qdec/Untitled/qdec.fsgd dods --glmdir /Users/dolphinede/Desktop/Probanden/qdec/Untitled --surf fsaverage lh --label /Users/dolphinede/Desktop/Probanden/fsaverage/label/lh.aparc.label --C /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-pial_lgi-Alter2-Cor.mat
- The FSGD file (if using one)
- And the design matrix above
Error in Analyze: command failed: mri_glmfit --y /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh --fsgd /Users/dolphinede/Desktop/Probanden/qdec/Untitled/qdec.fsgd dods --glmdir /Users/dolphinede/Desktop/Probanden/qdec/Untitled --surf fsaverage lh --label /Users/dolphinede/Desktop/Probanden/fsaverage/label/lh.aparc.label --C /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-pial_lgi-Alter2-Cor.mat
Best wishes
Daniel
-----Ursprüngliche Mitteilung----- Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: freesurfer freesurfer@nmr.mgh.harvard.edu Verschickt: Di, 24 Sept 2013 9:35 pm Betreff: Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
Hi Daniel, you can do this the way that you have specified, but, as you point out, one of the covariates will have to be a nuisance variable, meaning that it will not get tested. If you need to test all 3, then you'll have to use mri_glmfit with and FSGD file doug
On 09/24/2013 05:39 AM, Daniel Klein wrote:
Dear FreeSurfer experts,
I want to test linear, square and cubic effects of age on different parameters (thickness, lGI....) with qdec.
I add age (square) and age (cubic) as column in my qdec table.
Am i right to see only the square effects: Add Age square as continous factor and age (maybe age cubic too?) as nuisance factor in the model.
Best wishes and thanks a lot.
Daniel
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