Hi Doug, Below is the output in the terminal window from running the analysis to the crash. Attached are the qdec.fsgd and y.fsgd files from the qdec output. I'm not actually sure what these file represent - could you enlighten me?
Thanks!
Laura.
Number of subjects: 55
Number of factors: 48 (2 discrete, 46 continuous)
Number of classes: 4
Number of regressors: 188
============================================================
WARNING: will exclude subject 27115 from analysis due to NaN data point!
WARNING: will exclude subject 27211 from analysis due to NaN data point!
WARNING: will exclude subject 27212 from analysis due to NaN data point!
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
Nuisance factors: IntraCranialVol
1.000 1.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-CPT_IP-Cor -----------------------
Does the correlation between thickness and CPT_IP, accounting for group,
differ from zero?
Nuisance factors: IntraCranialVol
0.000 0.000 1.000 1.000 0.000 0.000;
lh-Diff-HC-SZ-Intercept-thickness -----------------------
Does the average thickness differ between HC and SZ?
Nuisance factors: IntraCranialVol
1.000 -1.000 0.000 0.000 0.000 0.000;
lh-Diff-HC-SZ-Cor-thickness-CPT_IP -----------------------
Does the thickness--CPT_IP correlation differ between HC and SZ?
Nuisance factors: IntraCranialVol
0.000 0.000 1.000 -1.000 0.000 0.000;
ninputs = 52
Checking inputs
nframestot = 52
Allocing output
Done allocing
nframes = 52
Writing to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
gdfReadHeader: reading
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 CPT_IP 2.83135 0.695203
1 IntraCranialVol 1.29955e+06 249396
Class Means of each Continuous Variable
1 groupHC 3.0515 1340186.4398
2 groupSZ 2.5936 1255661.8075
INFO: gd2mtx_method is dods
Reading source surface
/ncf/snp/04/SCORE/freesurfer_analysis/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 /ncf/snp/04/SCORE/freesurfer_analysis/qdec
cmdline mri_glmfit --y
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
--fsgd
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
dods --glmdir
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
--surf fsaverage lh --label
/ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat
--C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat
--C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat
--C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat
sysname Linux
hostname ncfws17.rc.fas.harvard.edu
machine x86_64
user ltully
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
logyflag 0
usedti 0
FSGD
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
labelmask
/ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
Loading y from
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/Xg.dat
Normalized matrix condition is 263.453
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 0.000000
Found 148025 voxels in mask
Saving mask to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/mask.mgh
Reshaping mriglm->mask...
search space = 73649.347769
DOF = 46
Starting fit and test
Fit completed in 0.11535 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.996105, ar1std=0.001362, gstd=6.478212, fwhm=15.255024
Writing results
lh-Avg-Intercept-thickness
maxvox sig=21.5032 F=315.736 at index 99361 0 0 seed=1330929601
lh-Avg-thickness-CPT_IP-Cor
maxvox sig=3.23567 F=13.661 at index 155907 0 0 seed=1330929601
lh-Diff-HC-SZ-Intercept-thickness
maxvox sig=-2.63051 F=10.3802 at index 6941 0 0 seed=1330929601
lh-Diff-HC-SZ-Cor-thickness-CPT_IP
maxvox sig=-3.05362 F=12.6489 at index 145301 0 0 seed=1330929601
mri_glmfit done
ninputs = 4
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Writing to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/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
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/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 CPT_IP 2.83135 0.695203
1 IntraCranialVol 1.29955e+06 249396
Class Means of each Continuous Variable
1 groupHC 3.0515 1340187.1111
2 groupSZ 2.5936 1255662.3200
MatrixMultiply: m1 is null!
No such file or directory
On Tue, Feb 28, 2012 at 5:51 PM, Douglas N Greve
<[email protected]>wrote:
> Can you send the fsgd file that is created? Also, please send more text
> output. It's hard to tell from a single line.
> doug
>
> Laura Tully wrote:
>
>> Hi,
>> I am trying to run a between group analysis in QDEC whilst controlling
>> for intrancranial volume. The design has one dichotomous variable (group2,
>> group2), one continuous (performance on behavioral task), and one nuisance
>> variable (intracranial volume). each time I run it qec crashes with the
>> following error:
>> MatrixMultiply: ml null!
>>
>> What does this error mean and how can I fix it?
>> What is odd is that this error does not seem to be consistently
>> reproducible - after successfully running the analyses without controlling
>> for ICV, I was then able to run it with ICV as a nuisance factor.
>> Thank you!
>> Laura.
>> --
>> Laura Tully
>> Social Neuroscience & Psychopathology
>> Harvard University
>> 806 William James Hall
>> 33 Kirkland St
>> Cambridge, MA 02138
>> [email protected] <mailto:[email protected]**>
>>
>>
>> ------------------------------**------------------------------**
>> ------------
>>
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>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [email protected]
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs:
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>
>
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--
Laura Tully
Social Neuroscience & Psychopathology
Harvard University
806 William James Hall
33 Kirkland St
Cambridge, MA 02138
[email protected]
+1 857 207 5509
y.fsgd
Description: Binary data
qdec.fsgd
Description: Binary data
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