Error with mri_glmfit command

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Martin Juneja

23 May 2019 23 May '19

8:43 p.m.

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Hi FS experts,

I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates).

My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Age

Input S001 Male 120 103 109 124 113 94 113 36

Input S003 Male 91 101 86 103 109 95 96 29

Input S004 Male 104 116 110 96 115 108 112 39

Input S005 Female 116 114 103 127 115 106 118 32

Input S006 Female 93 100 90 100 117 90 97 23

Input S008 Male 70 80 80 66 78 83 71 40

Input S009 Female 125 114 115 125 118 104 124 45

Input S010 Female 96 91 93 101 91 92 94 42

Input S011 Male 104 92 97 111 84 103 98 45

Input S012 Female 79 81 90 74 82 80 78 22

Input S014 Male 120 94 118 114 105 87 107 44

Input S015 Female 94 86 92 100 80 93 88 29

Input S016 Male 98 92 107 88 95 90 95 33

Input S017 Female 96 100 112 83 95 104 99 21

Input S018 Male 98 93 96 103 104 87 96 42

Input S019 Female 105 120 99 110 113 114 114 26

Input S020 Female 105 107 104 103 113 100 109 27

Input S022 Female 116 98 115 111 111 89 109 25

Input S023 Female 98 91 94 105 86 96 94 21

Input S024 Male 116 101 119 105 90 112 111 43

Input S025 Female 143 102 134 129 110 95 120 21

Input S028 Female 72 80 77 71 82 78 71 41

Input S029 Male 104 100 116 92 94 105 104 25

Input S030 Female 120 96 115 116 103 92 109 18

Input S031 Female 114 103 111 111 99 105 112 29

Input S033 Male 121 99 108 127 104 96 111 20

Input S035 Male 112 104 104 115 103 103 110 20

Input S036 Female 111 103 103 113 106 98 109 28

Input S037 Male 108 91 108 103 92 91 99 30

Input S038 Male 103 99 102 102 117 89 103 18

Input S039 Male 106 114 116 94 112 107 112 21

Input S040 Male 99 98 97 102 94 100 99 41

Input S041 Male 103 109 97 109 110 103 109 26 My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0

After I run mri_glmfit command, I get following error:

ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

--------------------------------

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

I would really appreciate any help in figuring out this issue.

Thanks, MJ

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Greve, Douglas N.,Ph.D.

24 May 24 May

10:29 a.m.

Can you send the Xg.dat file?

On 5/23/2019 8:43 PM, Martin Juneja wrote:

External Email - Use Caution

Hi FS experts,

I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates).

My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Age

Input S001 Male 120 103 109 124 113 94 113 36

Input S003 Male 91 101 86 103 109 95 96 29

Input S004 Male 104 116 110 96 115 108 112 39

Input S005 Female 116 114 103 127 115 106 118 32

Input S006 Female 93 100 90 100 117 90 97 23

Input S008 Male 70 80 80 66 78 83 71 40

Input S009 Female 125 114 115 125 118 104 124 45

Input S010 Female 96 91 93 101 91 92 94 42

Input S011 Male 104 92 97 111 84 103 98 45

Input S012 Female 79 81 90 74 82 80 78 22

Input S014 Male 120 94 118 114 105 87 107 44

Input S015 Female 94 86 92 100 80 93 88 29

Input S016 Male 98 92 107 88 95 90 95 33

Input S017 Female 96 100 112 83 95 104 99 21

Input S018 Male 98 93 96 103 104 87 96 42

Input S019 Female 105 120 99 110 113 114 114 26

Input S020 Female 105 107 104 103 113 100 109 27

Input S022 Female 116 98 115 111 111 89 109 25

Input S023 Female 98 91 94 105 86 96 94 21

Input S024 Male 116 101 119 105 90 112 111 43

Input S025 Female 143 102 134 129 110 95 120 21

Input S028 Female 72 80 77 71 82 78 71 41

Input S029 Male 104 100 116 92 94 105 104 25

Input S030 Female 120 96 115 116 103 92 109 18

Input S031 Female 114 103 111 111 99 105 112 29

Input S033 Male 121 99 108 127 104 96 111 20

Input S035 Male 112 104 104 115 103 103 110 20

Input S036 Female 111 103 103 113 106 98 109 28

Input S037 Male 108 91 108 103 92 91 99 30

Input S038 Male 103 99 102 102 117 89 103 18

Input S039 Male 106 114 116 94 112 107 112 21

Input S040 Male 99 98 97 102 94 100 99 41

Input S041 Male 103 109 97 109 110 103 109 26

My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0

After I run mri_glmfit command, I get following error:

ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

--------------------------------

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

I would really appreciate any help in figuring out this issue.

Thanks, MJ

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Martin Juneja

12:42 p.m.

External Email - Use Caution

Hi Dough,

Please find the Xg.dat file attached here.

Thanks.

On Fri, May 24, 2019 at 7:30 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

...

Can you send the Xg.dat file?

On 5/23/2019 8:43 PM, Martin Juneja wrote:
    External Email - Use Caution
Hi FS experts,

I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates).

My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Age

Input S001 Male 120 103 109 124 113 94 113 36

Input S003 Male 91 101 86 103 109 95 96 29

Input S004 Male 104 116 110 96 115 108 112 39

Input S005 Female 116 114 103 127 115 106 118 32

Input S006 Female 93 100 90 100 117 90 97 23

Input S008 Male 70 80 80 66 78 83 71 40

Input S009 Female 125 114 115 125 118 104 124 45

Input S010 Female 96 91 93 101 91 92 94 42

Input S011 Male 104 92 97 111 84 103 98 45

Input S012 Female 79 81 90 74 82 80 78 22

Input S014 Male 120 94 118 114 105 87 107 44

Input S015 Female 94 86 92 100 80 93 88 29

Input S016 Male 98 92 107 88 95 90 95 33

Input S017 Female 96 100 112 83 95 104 99 21

Input S018 Male 98 93 96 103 104 87 96 42

Input S019 Female 105 120 99 110 113 114 114 26

Input S020 Female 105 107 104 103 113 100 109 27

Input S022 Female 116 98 115 111 111 89 109 25

Input S023 Female 98 91 94 105 86 96 94 21

Input S024 Male 116 101 119 105 90 112 111 43

Input S025 Female 143 102 134 129 110 95 120 21

Input S028 Female 72 80 77 71 82 78 71 41

Input S029 Male 104 100 116 92 94 105 104 25

Input S030 Female 120 96 115 116 103 92 109 18

Input S031 Female 114 103 111 111 99 105 112 29

Input S033 Male 121 99 108 127 104 96 111 20

Input S035 Male 112 104 104 115 103 103 110 20

Input S036 Female 111 103 103 113 106 98 109 28

Input S037 Male 108 91 108 103 92 91 99 30

Input S038 Male 103 99 102 102 117 89 103 18

Input S039 Male 106 114 116 94 112 107 112 21

Input S040 Male 99 98 97 102 94 100 99 41

Input S041 Male 103 109 97 109 110 103 109 26 My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0

After I run mri_glmfit command, I get following error:

ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

I would really appreciate any help in figuring out this issue.

Thanks, MJ

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Martin Juneja

30 May 30 May

12:53 p.m.

External Email - Use Caution

Dear Douglas, Bruce (and FS experts),

I was just wondering if you got a chance to look at the Xg.dat file attached in my previous email. I would really appreciate any help in resolving the following error I get after I run mri_glmfit command:

ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

--------------------------------

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

Thanks.

On Fri, May 24, 2019 at 9:42 AM Martin Juneja mj70481@gmail.com wrote:

...

Hi Dough,

Please find the Xg.dat file attached here.

Thanks.

On Fri, May 24, 2019 at 7:30 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

...
Can you send the Xg.dat file?

On 5/23/2019 8:43 PM, Martin Juneja wrote:
    External Email - Use Caution
Hi FS experts,

I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates).

My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Age

Input S001 Male 120 103 109 124 113 94 113 36

Input S003 Male 91 101 86 103 109 95 96 29

Input S004 Male 104 116 110 96 115 108 112 39

Input S005 Female 116 114 103 127 115 106 118 32

Input S006 Female 93 100 90 100 117 90 97 23

Input S008 Male 70 80 80 66 78 83 71 40

Input S009 Female 125 114 115 125 118 104 124 45

Input S010 Female 96 91 93 101 91 92 94 42

Input S011 Male 104 92 97 111 84 103 98 45

Input S012 Female 79 81 90 74 82 80 78 22

Input S014 Male 120 94 118 114 105 87 107 44

Input S015 Female 94 86 92 100 80 93 88 29

Input S016 Male 98 92 107 88 95 90 95 33

Input S017 Female 96 100 112 83 95 104 99 21

Input S018 Male 98 93 96 103 104 87 96 42

Input S019 Female 105 120 99 110 113 114 114 26

Input S020 Female 105 107 104 103 113 100 109 27

Input S022 Female 116 98 115 111 111 89 109 25

Input S023 Female 98 91 94 105 86 96 94 21

Input S024 Male 116 101 119 105 90 112 111 43

Input S025 Female 143 102 134 129 110 95 120 21

Input S028 Female 72 80 77 71 82 78 71 41

Input S029 Male 104 100 116 92 94 105 104 25

Input S030 Female 120 96 115 116 103 92 109 18

Input S031 Female 114 103 111 111 99 105 112 29

Input S033 Male 121 99 108 127 104 96 111 20

Input S035 Male 112 104 104 115 103 103 110 20

Input S036 Female 111 103 103 113 106 98 109 28

Input S037 Male 108 91 108 103 92 91 99 30

Input S038 Male 103 99 102 102 117 89 103 18

Input S039 Male 106 114 116 94 112 107 112 21

Input S040 Male 99 98 97 102 94 100 99 41

Input S041 Male 103 109 97 109 110 103 109 26 My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0

After I run mri_glmfit command, I get following error:

ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

I would really appreciate any help in figuring out this issue.

Thanks, MJ

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Greve, Douglas N.,Ph.D.

1:08 p.m.

It could be a couple of things: 1. Your covariates have a large scale. You can try demeaning and dividing by the stddev to bring them into the range of 1.0 2. It looks like your covariates are highly correlated. You may need to reduce them or do a component analysis.

On 5/30/19 12:53 PM, Martin Juneja wrote:

...

External Email - Use Caution

Dear Douglas, Bruce (and FS experts),

ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

Thanks.

On Fri, May 24, 2019 at 9:42 AM Martin Juneja <mj70481@gmail.com mailto:mj70481@gmail.com> wrote:

Hi Dough,

Please find the Xg.dat file attached here.

Thanks.

On Fri, May 24, 2019 at 7:30 AM Greve, Douglas N.,Ph.D.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:

    Can you send the Xg.dat file?

    On 5/23/2019 8:43 PM, Martin Juneja wrote:

...

            External Email - Use Caution

    Hi FS experts,

    I want to find clusters showing an association between
    cortical measures and behavior x6 (sex, age and variables
    x1-x5 as covariates).

    My FSGD file looks like:
    GroupDescriptorFile 1
    Class Male
    Class Female
    Variables x1 x2 x3 x4 x5 x6 Age

    InputS001Male1201031091241139411336

    InputS003Male9110186103109959629

    InputS004Male1041161109611510811239

    InputS005Female11611410312711510611832

    InputS006Female9310090100117909723

    InputS008Male7080806678837140

    InputS009Female12511411512511810412445

    InputS010Female96919310191929442

    InputS011Male1049297111841039845

    InputS012Female7981907482807822

    InputS014Male120941181141058710744

    InputS015Female94869210080938829

    InputS016Male98921078895909533

    InputS017Female9610011283951049921

    InputS018Male989396103104879642

    InputS019Female1051209911011311411426

    InputS020Female10510710410311310010927

    InputS022Female116981151111118910925

    InputS023Female98919410586969421

    InputS024Male1161011191059011211143

    InputS025Female1431021341291109512021

    InputS028Female7280777182787141

    InputS029Male104100116929410510425

    InputS030Female120961151161039210918

    InputS031Female1141031111119910511229

    InputS033Male121991081271049611120

    InputS035Male11210410411510310311020

    InputS036Female1111031031131069810928

    InputS037Male1089110810392919930

    InputS038Male103991021021178910318

    InputS039Male1061141169411210711221

    InputS040Male999897102941009941

    InputS041Male1031099710911010310926

    My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5
    0.5 0 0

    After I run mri_glmfit command, I get following error:

    ERROR: matrix is ill-conditioned or badly scaled, condno = 385372

    --------------------------------

    Possible problem with experimental design:

    Check for duplicate entries and/or lack of range of

    continuous variables within a class.


    I would really appreciate any help in figuring out this issue.

    Thanks,
    MJ


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Greve, Douglas N.,Ph.D.
Martin Juneja