Can you resend the design matrix?
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
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
>
> 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
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> <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
>> > 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>
>>
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>> Outgoing:
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>>
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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