Re: [Freesurfer] group wrfx error: MRInormWeights: value less than or eq to 0.

Try the version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_concat doug

Sid Kundu wrote:

Hi Doug,

The --prune argument doesn't work with mri_concat in the version of freesurfer I am using. Any other way to accomplish this? _________________________________ Sid Kundu Biomedical Engineering Boston University

On Wed, Jan 25, 2012 at 3:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I'm guessing that there is a voxel (or more) in cesvar that is 0
for a subject (or more). Usually such voxels are masked out by
pruning the input ces. You can create your own mask with

mri_concat tal.cs.nii tal.cesvar.nii --prune --o junk.mgh
mri_binarize --i junk.mgh --min .00000000000001 --o newmask.mgh

Then pass this mask to mri_glmfit with the --mask option.

doug

Finnegan Calabro wrote:

    Hi Doug et al,

    We're running into a problem doing a wrfx group analysis using
    FreeSurfer 4.5.  Looks like the glmfit is having trouble with
    the weights.  We tried running it for different subsets of our
    subjects, and get the same thing, so it's not one subject
    contaminating the analysis.  Any guess where we should look
    for tracking this down?  Presumably the cesvar files are
    screwed up somehow, which would imply something went wrong in
    the individual selxavg3's.  But any ideas about what could
    lead to this?  The individual overlays all seem to look ok.



    [sidkundu@brodmann all-vs-null]$ mri_glmfit --y tal.ces.nii
    --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii
    --wls tal.cesvar.nii
    $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
    cwd
    /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null
    cmdline mri_glmfit --y tal.ces.nii --osgm --glmdir
    tal.wrfx.osgm --nii --mask ../tal.mask.nii --wls
    tal.cesvar.nii sysname  Linux
    hostname brodmann.bu.edu <http://brodmann.bu.edu>
    <http://brodmann.bu.edu/>

    machine  x86_64
    user     sidkundu
    FixVertexAreaFlag = 1
    UseMaskWithSmoothing     1
    OneSampleGroupMean 1
    y  
     /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii
    logyflag 0
    usedti  0
    mask ../tal.mask.nii
    maskinv 0
    glmdir tal.wrfx.osgm
    IllCondOK 0
    DoFFx 0
    wFile tal.cesvar.nii
    weightinv  1
    weightsqrt 1
    Creating output directory tal.wrfx.osgm
    Loading y from
    /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii
    Saving design matrix to tal.wrfx.osgm/Xg.dat
    Matrix condition is 1
    Pruning voxels by thr: 0.000000
    Found 260736 voxels in mask
    Saving mask to tal.wrfx.osgm/mask.nii
    search space = 2.08589e+06
    ERROR: MRInormWeights: value less than or eq to 0.
     c=34, r=2, s=33, v=0


-- 
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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