I don't know what is going on with that, but one thing you should do is
to normalize the eTIV (ie, remove it's mean and divide by the std dev).
Also, why are you including eTIV in the first place? Thickness does not
change with head size, only volume and surface area.
doug
On 7/24/15 2:34 AM, Dr Sampada Sinha wrote:
Dear Freesurfer experts,
Thanks for your valuable input. Since, comparison with global
thickness does not provide any valuable information we have decided
to forego the average thickness and lh-thickness comparison and now
added eTIV as another covariate with age
and
lh/rh thickess (
please see the attached .table.dat and the created
fsgd file with this mail). I was facing an error while trying to run
the qdec with eTIV as a covariate so I searched the forum and
followed the same instructions
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19987.html)
t
hat Dr Schmansky said over the same issue. But still, I am getting the
same error of /"MatrixMultiply: m1 is null!/ /No such file or
directory/". My error log on my the terminal says the following:
/
1 Gender discrete 2
1 Male
2 Female
2 Age continuous 0
3 lh-thickness continuous 0
4 eTIV continuous 0
5 EstimatedTotalIntraCranialVol continuous 0
Continuous Factors: Mean: StdDev:
------------------- ----- -------
Age 33.320 10.566
lh-thickness 2.201 0.306
eTIV 1229696.542 246342.246
EstimatedTotalIntraCranialVol 1229696.542 246342.246
Number of subjects: 25
Number of factors: 5 (1 discrete, 4 continuous)
Number of classes: 2
Number of regressors: 10
============================================================
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
1.000 1.000 0.000 0.000;
lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor -----------------------
Does the correlation between thickness and
EstimatedTotalIntraCranialVol, accounting for Gender, differ from zero?
0.000 0.000 1.000 1.000;
lh-Diff-Male-Female-Intercept-thickness -----------------------
Does the average thickness differ between Male and Female?
1.000 -1.000 0.000 0.000;
lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol
-----------------------
Does the thickness--EstimatedTotalIntraCranialVol correlation differ
between Male and Female?
0.000 0.000 1.000 -1.000;
ninputs = 25
Checking inputs
nframestot = 25
Allocing output
Done allocing
nframes = 25
Writing to /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh
gdfReadHeader: reading /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 EstimatedTotalIntraCranialVol 1.2297e+06 241365
Class Means of each Continuous Variable
1 GenderMale 1307770.0139
2 GenderFemale 1028936.1875
INFO: gd2mtx_method is dods
Reading source surface /home/anup/Desktop/QDEC/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 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/anup/Desktop/QDEC
cmdline mri_glmfit --y /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh
--fsgd /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd dods --glmdir
/home/anup/Desktop/QDEC/qdec/Untitled --surf fsaverage lh --label
/home/anup/Desktop/QDEC/fsaverage/label/lh.aparc.label --C
/home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor.mat
--C
/home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat
--C
/home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol.mat
sysname Linux
hostname localhost.localdomain
machine x86_64
user anup
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh
logyflag 0
usedti 0
FSGD /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd
labelmask /home/anup/Desktop/QDEC/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /home/anup/Desktop/QDEC/qdec/Untitled
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /home/anup/Desktop/QDEC/qdec/Untitled
Loading y from /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /home/anup/Desktop/QDEC/qdec/Untitled/Xg.dat
Normalized matrix condition is 147.732
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/anup/Desktop/QDEC/qdec/Untitled/mask.mgh
Reshaping mriglm->mask...
search space = 73649.347769
DOF = 21
Starting fit and test
Fit completed in 0.0211 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.998310, ar1std=0.001122, gstd=9.841412, fwhm=23.174754
Writing results
lh-Avg-Intercept-thickness
maxvox sig=10.1323 F=143.803 at index 23648 0 0 seed=1438013578
lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor
maxvox sig=-3.89264 F=21.9015 at index 54769 0 0 seed=1438013578
lh-Diff-Male-Female-Intercept-thickness
maxvox sig=-2.27889 F=9.69149 at index 12936 0 0 seed=1438013578
lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol
maxvox sig=2.39998 F=10.4556 at index 12936 0 0 seed=1438013578
mri_glmfit done
ninputs = 4
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Writing to /home/anup/Desktop/QDEC/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/anup/Desktop/QDEC/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 EstimatedTotalIntraCranialVol 1.2297e+06 241365
Class Means of each Continuous Variable
1 GenderMale 1307769.2222
2 GenderFemale 1028935.5714
MatrixMultiply: m1 is null!
No such file or directory/
Will you please let me know what is going wrong with my analysis?
Forever appreciateve and grateful for your responses!
Thanks and regards,
Sampada
AIIMS, New Delhi
*/
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