Hello Doug or Bruce, I demeaned and normalize like you suggested but I'm still getting the same results. I created a new fsgd file using the demeaned and normalized variables (n = (x-mean)/std(x). Any reason why? Thank you very much. Paul
On Fri, Jul 22, 2016 at 6:43 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Try demeaning and normalizing your continuous covariates in the FSGD file.
On 07/22/2016 06:17 PM, miracle ozzoude wrote:
Hello doug,
while running the mir_glmfit problem, i encountered this problem “
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
1 Education 15.5625 1.99902
2 Firstscore 1.03375 0.341785
3 Secondscore 1.03906 0.370678
4 Thirdscore 1.13844 0.4768
5 Averagescore 1.07375 0.364046
Class Means of each Continuous Variable
1 Group1 35.6316 15.0526 1.0342 1.2111 1.4289 1.2305
2 Group2 46.2308 16.3077 1.0331 0.7877 0.7138 0.8446
INFO: gd2mtx_method is dods
Reading source surface /Users/paul/Desktop/improvervsdeclinermri/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 /Users/paul/Desktop/improvervsdeclinermri
cmdline mri_glmfit --y lh.new.MOT.thickness.10B.mgh --fsgd new.MOT.fsgd dods --C new.firstmatrix.mtx --C new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf fsaverage lh --cortex --glmdir lh.new.MOT.glmdir
sysname Darwin
hostname TC-CT-LAB4-iMAC.local
machine x86_64
user paul
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/paul/Desktop/improvervsdeclinermri/lh.new.MOT.thickness.10B.mgh
logyflag 0
usedti 0
FSGD new.MOT.fsgd
labelmask /Users/paul/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.new.MOT.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.new.MOT.glmdir
Loading y from /Users/paul/Desktop/improvervsdeclinermri/lh.new.MOT.thickness.10B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to lh.new.MOT.glmdir/Xg.dat
Normalized matrix condition is 1.27568e+06
Design matrix ------------------
1.000 0.000 23.000 0.000 15.000 0.000 1.680 0.000 1.780 0.000 2.110 0.000 1.860 0.000;
1.000 0.000 43.000 0.000 16.000 0.000 0.840 0.000 0.890 0.000 1.190 0.000 0.970 0.000;
1.000 0.000 39.000 0.000 17.000 0.000 0.790 0.000 0.840 0.000 1.220 0.000 0.950 0.000;
1.000 0.000 19.000 0.000 13.000 0.000 0.840 0.000 1.060 0.000 1.260 0.000 1.050 0.000;
1.000 0.000 28.000 0.000 13.000 0.000 1.060 0.000 1.120 0.000 1.370 0.000 1.180 0.000
…………………………………………………………………………………………………………………...
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.27568e+06
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
- Your command line:
mri_glmfit --y lh.new.MOT.thickness.10B.mgh --fsgd new.MOT.fsgddods --C new.firstmatrix.mtx —C new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf fsaverage lh --cortex --glmdir lh.new.MOT.glmdir
The FSGD file (if using one)
And the design matrix above”
Below are my fsgd file and contrast matrix. I can’t add DeMeanFlag 1 because I am using dods and interested in group difference. Also, none of the responses from people with similar error helped me. I am using version 5.1
Thank you very much.
Paul
GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age Education Firstscore Secondscore Thirdscore Averagescore
Input 01053p/fsdir Group1 23 15 1.68 1.78 2.11 1.86
Input 01054p/fsdir Group1 43 16 0.84 0.89 1.19 0.97
Input 01061p/fsdir Group1 39 17 0.79 0.84 1.22 0.95
Input 01062p/fsdir Group1 19 13 0.84 1.06 1.26 1.05
Input 01074p/fsdir Group1 28 13 1.06 1.12 1.37 1.18
Input 01080p/fsdir Group1 28 18 0.97 1.26 1.33 1.19
Input 01099p/fsdir Group1 37 16 0.87 1.15 1.37 1.13
Input 01101p/fsdir Group1 20 14 1.00 1.37 1.45 1.27
Input 01102p/fsdir Group1 58 16 0.97 1.12 1.41 1.27
Input 01121p/fsdir Group1 28 18 0.87 1.00 1.00 0.96
Input 01127p/fsdir Group1 46 16 0.77 1.06 1.58 1.14
Input 01128p/fsdir Group1 21 16 1.58 1.78 1.78 1.71
Input 01130p/fsdir Group1 22 16 1.50 1.22 1.63 1.45
Input 01131p/fsdir Group1 19 13 1.54 1.68 2.11 1.78
Input 01141p/fsdir Group1 17 12 1.00 1.09 1.30 1.13
Input 1044pp/fsdir Group1 51 16 0.94 1.54 1.68 1.39
Input 1053pp/fsdir Group1 44 16 1.22 1.30 1.50 1.34
Input 1058pp/fsdir Group1 78 12 0.61 1.12 1.15 0.96
Input 1060pp/fsdir Group1 56 13 0.60 0.63 0.71 0.65
Input 01047p/fsdir Group2 50 18 1.12 0.94 0.94 1.00
Input 01075p/fsdir Group2 20 15 1.12 0.84 0.60 0.85
Input 01077p/fsdir Group2 48 16 0.43 0.35 0.35 0.38
Input 01091p/fsdir Group2 23 16 1.58 1.22 1.22 1.34
Input 01096p/fsdir Group2 17 17 1.50 1.26 1.19 1.32
Input 01113p/fsdir Group2 51 18 0.75 0.69 0.60 0.68
Input 01124p/fsdir Group2 43 18 1.33 0.89 0.87 1.03
Input 01134p/fsdir Group2 59 16 0.82 0.60 0.60 0.67
Input 1004pp/fsdir Group2 46 19 0.82 0.79 0.71 0.77
Input 1040pp/fsdir Group2 64 13 0.92 0.55 0.46 0.64
Input 1043pp/fsdir Group2 49 16 1.58 1.03 0.89 1.17
Input 1064pp/fsdir Group2 78 12 0.40 0.11 0.10 0.20
Input 1067pp/fsdir Group2 53 18 1.06 0.97 0.75 0.93
first contrast matrix
1 -1 0 0 0 0 0 0 0 0 0 0 0 0
group1 greater than group 2 regressing out age, education, first, second, third and average
second constrast matrix
-1 1 0 0 0 0 0 0 0 0 0 0 0 0
group 2 greater than group 1 regressing out age, education, first, second, third and average
third contrast matrix
0 0 0 0 0 0 0.5 -0.5 0 0 0 0 0 0
group 1 showing increasing correlation with first score compared to group 2
fourth contrast matrix
0 0 0 0 0 0 -0.5 0.5 0 0 0 0 0 0
group2 showing showing increasing correlation with first score compared to group 1
fifth contrast matrix
0 0 0 0 0 0 0 0 0.5 -0.5 0 0 0 0
group1 showing showing increasing correlation with second score compared to group 2
sixth contrast matrix
0 0 0 0 0 0 0 0 -0.5 0.5 0 0 0 0
group2 showing showing increasing correlation with second score compared to group 1
seventh contrast matrix
0 0 0 0 0 0 0 0 0 0 0.5 -0.5 0 0
group1 showing showing increasing correlation with third score compared to group 2
eighth contrast matrix
0 0 0 0 0 0 0 0 0 0 -0.5 0.5 0 0
group2 showing showing increasing correlation with third score compared to group 1
ninety contrast matrix
0 0 0 0 0 0 0 0 0 0 0 0 0.5 -0.5
group1 showing showing increasing correlation with average score compared to group 2
tenth contrast matrix
0 0 0 0 0 0 0 0 0 0 0 0 -0.5 0.5
group2 showing showing increasing correlation with average score compared to group 1
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