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

Yes, that does look excessive. There should be a "masks" volume that gets created. This will have the individual masks for each subject. You can load this something like

tksurfer fsaverage lh inflated -overlay masks.mgh -fthresh 0.5 -t masks.mgh

ie, load it as an overlay and timecourse. When you click on a point, the time course will show your the value at each subject, and you can look for subjects where it is 0.

You should also do this with the cesvar map (that's probably where your problem is).

doug

Sid Kundu wrote:

Hi Doug,

Thanks for the help, was able to get the group analysis to work. However, I went back and looked at the mask that was being created and passed into the glmfit and got what's shown in the attached pictures. The ammount of zero valued voxels seems really high. Not sure if this is out of the ordinary or not, but might indicate a problem somewhere else in my analysis. _________________________________ Sid Kundu Biomedical Engineering Boston University

On Thu, Jan 26, 2012 at 11:59 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
    <mailto: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>
           <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>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
       Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422
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       <tel:617-726-7422 <tel:617-726-7422>>

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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
<tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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