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:
1. Your command line:
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
2. The FSGD file (if using one)
3. 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you doug. Is there a command for normalising in fsgd file. I know DeMeaning is DeMeanFlag 1. Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Friday, July 22, 2016 6:45 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates
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.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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Can you send your new fsgd file and new design matrix?
On 7/24/16 6:06 PM, miracle ozzoude wrote:
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 mailto: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: > > 1. Your command line: > > 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 > > 2. The FSGD file (if using one) > > 3. 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 > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug, Sure. Here are my new fsgd file and new contrast matrix ( matrix is the same as the old one). Best, Paul GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Education Firstscore Secondscore Thirdscore Averagescore Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14 Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26 Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33 Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05 Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31 Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32 Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16 Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55 Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21 0.56 0.26 Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31 Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18 Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74 Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03 Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92 Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16 Input 1044pp/fsdir Group1 0.63 0.29 -0.27 1.33 1.12 0.86 Input 1053pp/fsdir Group1 0.23 0.29 0.54 0.69 0.75 0.73 Input 1058pp/fsdir Group1 2.16 -1.56 -1.22 0.21 0.02 -0.30 Input 1060pp/fsdir Group1 0.91 -1.10 -1.25 -1.09 -0.88 -1.15 Input 01047p/fsdir Group2 0.57 1.21 0.25 -0.26 -0.41 -0.19 Input 01075p/fsdir Group2 -1.13 -0.17 0.25 -0.53 -1.11 -0.59 Input 01077p/fsdir Group2 0.46 0.29 -1.74 -1.83 -1.63 -1.89 Input 01091p/fsdir Group2 -0.96 0.29 1.57 0.48 0.17 0.73 Input 01096p/fsdir Group2 -1.3 -2.02 1.34 0.59 0.11 0.67 Input 01113p/fsdir Group2 0.63 1.21 -0.82 -0.93 -1.11 -1.06 Input 01124p/fsdir Group2 0.17 1.21 0.85 -0.40 -0.55 -0.11 Input 01134p/fsdir Group2 1.08 0.29 -0.62 -1.17 -1.11 -1.08 Input 1004pp/fsdir Group2 0.34 1.67 -0.62 -0.66 -0.88 -0.81 Input 1040pp/fsdir Group2 1.37 -1.10 -0.33 -1.30 -1.40 -1.16 Input 1043pp/fsdir Group2 0.51 0.29 1.57 -0.02 -0.51 0.26 Input 1064pp/fsdir Group2 2.16 -1.56 -1.83 -2.47 -2.14 -2.36 Input 1067pp/fsdir Group2 0.74 1.21 0.08 -0.18 -0.80 -0.39
New Contrast Matrix
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
On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you send your new fsgd file and new design matrix?
On 7/24/16 6:06 PM, miracle ozzoude wrote:
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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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.
Can you resend the design matrix?
On 07/26/2016 11:46 AM, miracle ozzoude wrote:
Hello Doug, Sure. Here are my new fsgd file and new contrast matrix ( matrix is the same as the old one). Best, Paul GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Education Firstscore Secondscore Thirdscore Averagescore Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14 Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26 Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33 Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05 Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31 Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32 Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16 Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55 Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21 0.56 0.26 Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31 Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18 Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74 Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03 Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92 Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16 Input 1044pp/fsdir Group1 0.63 0.29 -0.27 1.33 1.12 0.86 Input 1053pp/fsdir Group1 0.23 0.29 0.54 0.69 0.75 0.73 Input 1058pp/fsdir Group1 2.16 -1.56 -1.22 0.21 0.02 -0.30 Input 1060pp/fsdir Group1 0.91 -1.10 -1.25 -1.09 -0.88 -1.15 Input 01047p/fsdir Group2 0.57 1.21 0.25 -0.26 -0.41 -0.19 Input 01075p/fsdir Group2 -1.13 -0.17 0.25 -0.53 -1.11 -0.59 Input 01077p/fsdir Group2 0.46 0.29 -1.74 -1.83 -1.63 -1.89 Input 01091p/fsdir Group2 -0.96 0.29 1.57 0.48 0.17 0.73 Input 01096p/fsdir Group2 -1.3 -2.02 1.34 0.59 0.11 0.67 Input 01113p/fsdir Group2 0.63 1.21 -0.82 -0.93 -1.11 -1.06 Input 01124p/fsdir Group2 0.17 1.21 0.85 -0.40 -0.55 -0.11 Input 01134p/fsdir Group2 1.08 0.29 -0.62 -1.17 -1.11 -1.08 Input 1004pp/fsdir Group2 0.34 1.67 -0.62 -0.66 -0.88 -0.81 Input 1040pp/fsdir Group2 1.37 -1.10 -0.33 -1.30 -1.40 -1.16 Input 1043pp/fsdir Group2 0.51 0.29 1.57 -0.02 -0.51 0.26 Input 1064pp/fsdir Group2 2.16 -1.56 -1.83 -2.47 -2.14 -2.36 Input 1067pp/fsdir Group2 0.74 1.21 0.08 -0.18 -0.80 -0.39
New Contrast Matrix
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
On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send your new fsgd file and new design matrix? On 7/24/16 6:06 PM, miracle ozzoude wrote: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 <mailto: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: > > 1. Your command line: > > 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 > > 2. The FSGD file (if using one) > > 3. 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 > > > > _______________________________________________ > 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. 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Here's my design matrix 1.000 0.000 -0.960 0.000 -0.170 0.000 1.860 0.000 1.970 0.000 2.010 0.000 2.140 0.000; 1.000 0.000 0.170 0.000 0.290 0.000 -0.560 0.000 -0.400 0.000 0.110 0.000 -0.260 0.000; 1.000 0.000 -0.050 0.000 0.750 0.000 -0.700 0.000 -0.530 0.000 0.170 0.000 -0.330 0.000; 1.000 0.000 -1.190 0.000 -1.100 0.000 -0.560 0.000 0.060 0.000 0.250 0.000 -0.050 0.000; 1.000 0.000 -0.680 0.000 -1.100 0.000 0.080 0.000 0.210 0.000 0.480 0.000 0.310 0.000; 1.000 0.000 -0.680 0.000 1.210 0.000 -0.180 0.000 0.590 0.000 0.400 0.000 0.320 0.000; 1.000 0.000 -0.170 0.000 0.290 0.000 -0.470 0.000 0.290 0.000 0.480 0.000 0.160 0.000; 1.000 0.000 -1.130 0.000 -0.630 0.000 -0.100 0.000 0.880 0.000 0.640 0.000 0.550 0.000; 1.000 0.000 1.030 0.000 0.290 0.000 -0.180 0.000 0.210 0.000 0.560 0.000 0.260 0.000; 1.000 0.000 -0.680 0.000 1.210 0.000 -0.470 0.000 -0.100 0.000 -0.290 0.000 -0.310 0.000; 1.000 0.000 0.340 0.000 0.290 0.000 -0.760 0.000 0.060 0.000 0.910 0.000 0.180 0.000; 1.000 0.000 -1.080 0.000 0.290 0.000 1.570 0.000 1.970 0.000 1.320 0.000 1.740 0.000; 1.000 0.000 -1.020 0.000 0.290 0.000 1.340 0.000 0.480 0.000 1.010 0.000 1.030 0.000; 1.000 0.000 -1.190 0.000 -1.100 0.000 1.460 0.000 1.700 0.000 2.010 0.000 1.920 0.000; 1.000 0.000 -1.300 0.000 -1.560 0.000 -0.100 0.000 0.140 0.000 0.330 0.000 0.160 0.000; 1.000 0.000 0.630 0.000 0.290 0.000 -0.270 0.000 1.330 0.000 1.120 0.000 0.860 0.000; 1.000 0.000 0.230 0.000 0.290 0.000 0.540 0.000 0.690 0.000 0.750 0.000 0.730 0.000; 1.000 0.000 2.160 0.000 -1.560 0.000 -1.220 0.000 0.210 0.000 0.020 0.000 -0.300 0.000; 1.000 0.000 0.910 0.000 -1.100 0.000 -1.250 0.000 -1.090 0.000 -0.880 0.000 -1.150 0.000; 0.000 1.000 0.000 0.570 0.000 1.210 0.000 0.250 0.000 -0.260 0.000 -0.410 0.000 -0.190; 0.000 1.000 0.000 -1.130 0.000 -0.170 0.000 0.250 0.000 -0.530 0.000 -1.110 0.000 -0.590; 0.000 1.000 0.000 0.460 0.000 0.290 0.000 -1.740 0.000 -1.830 0.000 -1.630 0.000 -1.890; 0.000 1.000 0.000 -0.960 0.000 0.290 0.000 1.570 0.000 0.480 0.000 0.170 0.000 0.730; 0.000 1.000 0.000 -1.300 0.000 -2.020 0.000 1.340 0.000 0.590 0.000 0.110 0.000 0.670; 0.000 1.000 0.000 0.630 0.000 1.210 0.000 -0.820 0.000 -0.930 0.000 -1.110 0.000 -1.060; 0.000 1.000 0.000 0.170 0.000 1.210 0.000 0.850 0.000 -0.400 0.000 -0.550 0.000 -0.110; 0.000 1.000 0.000 1.080 0.000 0.290 0.000 -0.620 0.000 -1.170 0.000 -1.110 0.000 -1.080; 0.000 1.000 0.000 0.340 0.000 1.670 0.000 -0.620 0.000 -0.660 0.000 -0.880 0.000 -0.810; 0.000 1.000 0.000 1.370 0.000 -1.100 0.000 -0.330 0.000 -1.300 0.000 -1.400 0.000 -1.160; 0.000 1.000 0.000 0.510 0.000 0.290 0.000 1.570 0.000 -0.020 0.000 -0.510 0.000 0.260; 0.000 1.000 0.000 2.160 0.000 -1.560 0.000 -1.830 0.000 -2.470 0.000 -2.140 0.000 -2.360; 0.000 1.000 0.000 0.740 0.000 1.210 0.000 0.080 0.000 -0.180 0.000 -0.800 0.000 -0.390;
On Tue, Jul 26, 2016 at 12:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Can you resend the design matrix?
On 07/26/2016 11:46 AM, miracle ozzoude wrote:
Hello Doug, Sure. Here are my new fsgd file and new contrast matrix ( matrix is the same as the old one). Best, Paul GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Education Firstscore Secondscore Thirdscore Averagescore Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14 Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26 Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33 Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05 Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31 Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32 Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16 Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55 Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21 0.56 0.26 Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31 Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18 Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74 Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03 Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92 Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16 Input 1044pp/fsdir Group1 0.63 0.29 -0.27 1.33 1.12 0.86 Input 1053pp/fsdir Group1 0.23 0.29 0.54 0.69 0.75 0.73 Input 1058pp/fsdir Group1 2.16 -1.56 -1.22 0.21 0.02 -0.30 Input 1060pp/fsdir Group1 0.91 -1.10 -1.25 -1.09 -0.88 -1.15 Input 01047p/fsdir Group2 0.57 1.21 0.25 -0.26 -0.41 -0.19 Input 01075p/fsdir Group2 -1.13 -0.17 0.25 -0.53 -1.11 -0.59 Input 01077p/fsdir Group2 0.46 0.29 -1.74 -1.83 -1.63 -1.89 Input 01091p/fsdir Group2 -0.96 0.29 1.57 0.48 0.17 0.73 Input 01096p/fsdir Group2 -1.3 -2.02 1.34 0.59 0.11 0.67 Input 01113p/fsdir Group2 0.63 1.21 -0.82 -0.93 -1.11 -1.06 Input 01124p/fsdir Group2 0.17 1.21 0.85 -0.40 -0.55 -0.11 Input 01134p/fsdir Group2 1.08 0.29 -0.62 -1.17 -1.11 -1.08 Input 1004pp/fsdir Group2 0.34 1.67 -0.62 -0.66 -0.88 -0.81 Input 1040pp/fsdir Group2 1.37 -1.10 -0.33 -1.30 -1.40 -1.16 Input 1043pp/fsdir Group2 0.51 0.29 1.57 -0.02 -0.51 0.26 Input 1064pp/fsdir Group2 2.16 -1.56 -1.83 -2.47 -2.14 -2.36 Input 1067pp/fsdir Group2 0.74 1.21 0.08 -0.18 -0.80 -0.39
New Contrast Matrix
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
On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send your new fsgd file and new design matrix? On 7/24/16 6:06 PM, miracle ozzoude wrote: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 <mailto: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 bedone.
> > 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: > > 1. Your command line: > > 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 > > 2. The FSGD file (if using one) > > 3. 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 EducationFirstscore
> 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 secondscore
> 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 secondscore
> 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 > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
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