Re: [Freesurfer] qdec and Intracranial volume correction - error message

Mahinda Yogarajah wrote:

Hi Doug,

Thanks for the response. I have had a read about demeaning on the forum. I had a couple of questions:

1. If I want to include age as well as ICV as nuisance variables in a

DODS analysis comparing thickness between patients and controls, should I demean (+ ? normalise) the age as well as the ICV.

Yes

2. Why the need to normalise as well as demean the ICV - I hadn't come

across this in the forums.

It might not be necessary. There is a mathematical problem that arises when the scale of the different columns is very different. In the end, it should have no effect on your results.

doug

Thanks.

Mahinda

On Mon, Feb 27, 2012 at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Mahinda, try demeaning and normalizing the ICV values (ie,
subtract the mean and divide by the stddev).
doug

Mahinda Yogarajah wrote:

    Dear Experts,

    I am trying to carry out a simple 2 group (conrol and patient)
    analysis with ICV as nuisance factor, and thickness as the
    dependent variable.

    However whenever I include ICV (inputed by following the qdec
    tutorial and the generate stats table) I get the following
    output and error message:
    ------------------------------------------------------------------

    lh-Avg-Intercept-thickness -----------------------

    Does the average thickness differ from zero?

     1.000   1.000   0.000   0.000;



    lh-Avg-thickness-IntraCranialVol-Cor -----------------------

    Does the correlation between thickness and IntraCranialVol,
    accounting for diagnosis, differ from zero?

     0.000   0.000   1.000   1.000;



    lh-Diff-Patients-Control-Intercept-thickness
    -----------------------

    Does the average thickness differ between Patients and Control?

     1.000  -1.000   0.000   0.000;



    lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol
    -----------------------

    Does the thickness--IntraCranialVol correlation differ between
    Patients and Control?

     0.000   0.000   1.000  -1.000;



    ninputs = 40

    Checking inputs

    nframestot = 40

    Allocing output

    Done allocing

    nframes = 40

    Writing to /home/myogaraj/freesurfer/qdec/Untitled/y.mgh

    gdfReadHeader: reading
    /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd

    INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

    Continuous Variable Means (all subjects)

    0 IntraCranialVol 1.42401e+06 259214

    Class Means of each Continuous Variable

    1 diagnosisPatients 1343236.0559 <tel:1343236.0559>

    2 diagnosisControl 1497089.0952

    INFO: gd2mtx_method is dods

    Reading source surface
    /home/myogaraj/freesurfer/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 /home/myogaraj/freesurfer/qdec

    cmdline mri_glmfit --y
    /home/myogaraj/freesurfer/qdec/Untitled/y.mgh --fsgd
    /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd dods
    --glmdir /home/myogaraj/freesurfer/qdec/Untitled --surf
    fsaverage lh --label
    /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label --C
    /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
    --C
    /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-thickness-IntraCranialVol-Cor.mat
    --C
    /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Intercept-thickness.mat
    --C
    /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol.mat


    sysname  Linux

    hostname localhost.localdomain

    machine  x86_64

    user     myogaraj

    FixVertexAreaFlag = 1

    UseMaskWithSmoothing     1

    OneSampleGroupMean 0

    y    /home/myogaraj/freesurfer/qdec/Untitled/y.mgh

    logyflag 0

    usedti  0

    FSGD /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd

    labelmask
     /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label

    maskinv 0

    glmdir /home/myogaraj/freesurfer/qdec/Untitled

    IllCondOK 0

    ReScaleX 1

    DoFFx 0

    Creating output directory /home/myogaraj/freesurfer/qdec/Untitled

    Loading y from /home/myogaraj/freesurfer/qdec/Untitled/y.mgh

    INFO: gd2mtx_method is dods

    Saving design matrix to
    /home/myogaraj/freesurfer/qdec/Untitled/Xg.dat

    Normalized matrix condition is 175.031

    Matrix condition is 1e+08

    Found 148151 points in label.

    Pruning voxels by thr: 0.000000

    Found 148025 voxels in mask

    Saving mask to /home/myogaraj/freesurfer/qdec/Untitled/mask.mgh

    Reshaping mriglm->mask...

    search space = 73649.347769

    DOF = 36

    Starting fit and test

    Fit completed in 0.0710833 minutes

    Computing spatial AR1 on surface

    Residual: ar1mn=0.995672, ar1std=0.001628, gstd=6.144582,
    fwhm=14.469384

    Writing results

     lh-Avg-Intercept-thickness

       maxvox sig=19.391  F=349.349  at  index 102911 0 0  
     seed=1330322022

     lh-Avg-thickness-IntraCranialVol-Cor

       maxvox sig=-3.43147  F=15.4402  at  index 109705 0 0  
     seed=1330322022

     lh-Diff-Patients-Control-Intercept-thickness

       maxvox sig=3.99329  F=19.0823  at  index 28994 0 0  
     seed=1330322022

     lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol

       maxvox sig=-3.79353  F=17.7548  at  index 129172 0 0  
     seed=1330322022

    mri_glmfit done

    ninputs = 4

    Checking inputs

    nframestot = 4

    Allocing output

    Done allocing

    nframes = 4

    Writing to
    /home/myogaraj/freesurfer/qdec/Untitled/contrasts.sig.mgh

    reading colortable from annotation file...

    colortable with 36 entries read (originally
    /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

    reading colortable from annotation file...

    colortable with 36 entries read (originally
    /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

    gdfReadHeader: reading
    /home/myogaraj/freesurfer/qdec/Untitled/y.fsgd

    INFO: ignoring tag Creator

    INFO: ignoring tag SUBJECTS_DIR

    INFO: ignoring tag SynthSeed

    INFO: NOT demeaning continuous variables

    Continuous Variable Means (all subjects)

    0 IntraCranialVol 1.42401e+06 259213

    Class Means of each Continuous Variable

    1 diagnosisPatients 1343236.3158 <tel:1343236.3158>

    2 diagnosisControl 1497089.0476

    MatrixMultiply: m1 is null!


    No such file or directory

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

    Can anyone advise ?

    Thanks.

    Mahinda


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-- 
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
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