Laura.

On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

If it's working with demeaning, then that was the problem. The subjects with NaNs are going to be excluded entirely as we have no way to estimate missing fields.
doug

Laura Tully wrote:

Hi Nick and Doug,
Thanks for the help, I'll give the demeaning a try.
Re: the missing values - all my missing data points are denoted with NaN so that I can include those subjects on the measures that they do have, but exclude them on measures they don't have (I think this is the only way to load the data table if there are missing values, is that correct?) This seems to be working fine when I do not include ICV as a nuisance variable. Do you think that these non-number cells are causing the issue? (I have check the data table to make sure that there are no empty cells).
Laura.
On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

In the terminal output, it says that it will exclude a subject
because there is a NaN data point. NaN = "not a number". Check
your data table to make sure that everything is ok.
doug

Nick Schmansky wrote:

it means to subtract the mean of the icv values from each.
that way the
values are close to zero, and closer in value to the other
values in the
glm (which seems to make the glm happier).

n.

On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote:

Hi Doug,

I saw on a previous mailing earlier this week that someone
has been
having a similar error and that your advice was to demean
the ICV. I
apologise if this is a stupid question, but what does it
mean to
"demean"? And, how do i do that?

Thanks in advance!

Laura.
On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully
<tully.laura@googlemail.com
<mailto:tully.laura@googlemail.com>> wrote:
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
<http://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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> 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
ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>

<mailto:ltully@fas.harvard.edu

<mailto:ltully@fas.harvard.edu>>
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-- Douglas
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MGH-NMR Center
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-- Laura Tully
Social Neuroscience & Psychopathology
Harvard University
806 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>
+1 857 207 5509 <tel:%2B1%20857%20207%205509>

-- Laura Tully
Social Neuroscience & Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>

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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
<tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

--
Laura Tully
Social Neuroscience & Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138

ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

--
Laura Tully
Social Neuroscience & Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltully@fas.harvard.edu