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=1330322022
lh-Avg-thickness-IntraCranialVol-Cor
maxvox sig=-3.43147 F=15.4402 at index 109705 0 0 seed=1330322022
lh-Diff-Patients-Control-Intercept-thickness
maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022
lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol
maxvox sig=-3.79353 F=17.7548 at index 129172 0 0 seed=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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the response. I have had a read about demeaning on the forum. I had a couple of questions:
1) If I want to include age as well as ICV as nuisance variables in a DODS analysis comparing thickness between patients and controls, should I demean (+ ? normalise) the age as well as the ICV.
2) Why the need to normalise as well as demean the ICV - I hadn't come across this in the forums.
Thanks.
Mahinda
On Mon, Feb 27, 2012 at 3:12 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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=1330322022
lh-Avg-thickness-**IntraCranialVol-Cor
maxvox sig=-3.43147 F=15.4402 at index 109705 0 0 seed=1330322022
lh-Diff-Patients-Control-**Intercept-thickness
maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022
lh-Diff-Patients-Control-Cor-**thickness-IntraCranialVol
maxvox sig=-3.79353 F=17.7548 at index 129172 0 0 seed=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
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Mahinda Yogarajah wrote:
Hi Doug,
Thanks for the response. I have had a read about demeaning on the forum. I had a couple of questions:
- If I want to include age as well as ICV as nuisance variables in a
DODS analysis comparing thickness between patients and controls, should I demean (+ ? normalise) the age as well as the ICV.
Yes
- Why the need to normalise as well as demean the ICV - I hadn't come
across this in the forums.
It might not be necessary. There is a mathematical problem that arises when the scale of the different columns is very different. In the end, it should have no effect on your results.
doug
Thanks.
Mahinda
On Mon, Feb 27, 2012 at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 <tel: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=1330322022 lh-Avg-thickness-IntraCranialVol-Cor maxvox sig=-3.43147 F=15.4402 at index 109705 0 0 seed=1330322022 lh-Diff-Patients-Control-Intercept-thickness maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022 lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol maxvox sig=-3.79353 F=17.7548 at index 129172 0 0 seed=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 <tel:1343236.3158> 2 diagnosisControl 1497089.0476 MatrixMultiply: m1 is null! No such file or directory --------------------------------------------------------- Can anyone advise ? Thanks. Mahinda ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Mahinda Yogarajah