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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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
>
>
>
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