Hi Mahinda, try demeaning and normalizing the ICV values (ie, subtract the mean and divide by the stddev). doug
Mahinda Yogarajah wrote:
Dear Experts,
I am trying to carry out a simple 2 group (conrol and patient) analysis with ICV as nuisance factor, and thickness as the dependent variable.
However whenever I include ICV (inputed by following the qdec tutorial and the generate stats table) I get the following output and error message:
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
1.000 1.000 0.000 0.000;
lh-Avg-thickness-IntraCranialVol-Cor -----------------------
Does the correlation between thickness and IntraCranialVol, accounting for diagnosis, differ from zero?
0.000 0.000 1.000 1.000;
lh-Diff-Patients-Control-Intercept-thickness -----------------------
Does the average thickness differ between Patients and Control?
1.000 -1.000 0.000 0.000;
lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol
Does the thickness--IntraCranialVol correlation differ between Patients and Control?
0.000 0.000 1.000 -1.000;
ninputs = 40
Checking inputs
nframestot = 40
Allocing output
Done allocing
nframes = 40
Writing to /home/myogaraj/freesurfer/qdec/Untitled/y.mgh
gdfReadHeader: reading /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 IntraCranialVol 1.42401e+06 259214
Class Means of each Continuous Variable
1 diagnosisPatients 1343236.0559
2 diagnosisControl 1497089.0952
INFO: gd2mtx_method is dods
Reading source surface /home/myogaraj/freesurfer/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /home/myogaraj/freesurfer/qdec
cmdline mri_glmfit --y /home/myogaraj/freesurfer/qdec/Untitled/y.mgh --fsgd /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/myogaraj/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-thickness-IntraCranialVol-Cor.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Intercept-thickness.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol.mat
sysname Linux
hostname localhost.localdomain
machine x86_64
user myogaraj
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/myogaraj/freesurfer/qdec/Untitled/y.mgh
logyflag 0
usedti 0
FSGD /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd
labelmask /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /home/myogaraj/freesurfer/qdec/Untitled
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /home/myogaraj/freesurfer/qdec/Untitled
Loading y from /home/myogaraj/freesurfer/qdec/Untitled/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /home/myogaraj/freesurfer/qdec/Untitled/Xg.dat
Normalized matrix condition is 175.031
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 0.000000
Found 148025 voxels in mask
Saving mask to /home/myogaraj/freesurfer/qdec/Untitled/mask.mgh
Reshaping mriglm->mask...
search space = 73649.347769
DOF = 36
Starting fit and test
Fit completed in 0.0710833 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995672, ar1std=0.001628, gstd=6.144582, fwhm=14.469384
Writing results
lh-Avg-Intercept-thickness
maxvox sig=19.391 F=349.349 at index 102911 0 0 seed=1330322022lh-Avg-thickness-IntraCranialVol-Cor
maxvox sig=-3.43147 F=15.4402 at index 109705 0 0seed=1330322022
lh-Diff-Patients-Control-Intercept-thickness
maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol
maxvox sig=-3.79353 F=17.7548 at index 129172 0 0seed=1330322022
mri_glmfit done
ninputs = 4
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Writing to /home/myogaraj/freesurfer/qdec/Untitled/contrasts.sig.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
gdfReadHeader: reading /home/myogaraj/freesurfer/qdec/Untitled/y.fsgd
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 IntraCranialVol 1.42401e+06 259213
Class Means of each Continuous Variable
1 diagnosisPatients 1343236.3158
2 diagnosisControl 1497089.0476
MatrixMultiply: m1 is null!
No such file or directory
Can anyone advise ?
Thanks.
Mahinda
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