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:
>
>   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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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