On 10/06/2009, at 9:51 PM, Toh Hock Wong wrote:
Hi all, I have reconstructed 12 paediatric subjects aged 4-13 and managed to load qdec as well as generating stats. The factors are age, diagnosis, gender and a continuos factor such as lh temporalpole thickness. When i click analyze, the return is a list of errors as follow. UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness/y.mgh
logyflag 0
usedti 0
FSGD /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness/qdec.fsgd
labelmask /Applications/freesurfer/subjects/fsaverage/label/ lh.cortex.label
maskinv 0
glmdir /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness
DoFFx 0
Creating output directory /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness
Loading y from /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness/y.mgh
Matrix condition is 1e+08
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.
1.000 0.000 0.000 0.000 3.701 0.000 0.000 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 4.554 0.000;
1.000 0.000 0.000 0.000 4.044 0.000 0.000 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 4.459 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 3.857 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 3.537 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 3.652 0.000;
1.000 0.000 0.000 0.000 2.870 0.000 0.000 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 3.736 0.000;
0.000 0.000 1.000 0.000 0.000 0.000 3.636 0.000;
1.000 0.000 0.000 0.000 4.102 0.000 0.000 0.000;
1.000 0.000 0.000 0.000 3.755 0.000 0.000 0.000;
0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.816;
Error in Analyze: command failed: mri_glmfit --y /Applications/ freesurfer/subjects/qdec/lh_temporalpole_thickness/y.mgh --fsgd / Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness --surf fsaverage lh --label /Applications/ freesurfer/subjects/fsaverage/label/lh.cortex.label --C / Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/ freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Avg- thickness-lh_temporalpole_thickness-Cor.mat --C /Applications/ freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Diff- nonepileptic-epilepsy-Intercept-thickness.mat --C /Applications/ freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Diff- nonepileptic-epilepsy-Cor-thickness-lh_temporalpole_thickness.mat -- C /Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C / Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ contrasts/lh-Diff-Male-Female-Cor-thickness- lh_temporalpole_thickness.mat --C /Applications/freesurfer/subjects/ qdec/lh_temporalpole_thickness/contrasts/lh-X-diagnosis-gender- Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/ lh_temporalpole_thickness/contrasts/lh-X-diagnosis-gender-Cor- thickness-lh_temporalpole_thickness.mat
What do i need to do from here?
Do i have to write a fsgd file/contrast etc? Any suggestions will be most appreciated!
If i wish to use freesurfer for a paediatric group less than 10 years old, what errors or difficulties should i be anticipating?
Thanks! Toh Wong