Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume - Freesurfer

13 Dec 2016


      Hi Doug,
My apologies for omitting the previous emails when replying earlier.
To create the sig.mgh file we used a volume specific mri_glmfit analysis, with volume specific inputs / no --hemi/hemis flag.
I don't know if this information is helpful but when we've run a nearly identical analysis (using almost all of the same participants and a slightly different covariate of interest) the volume came out completely fine. In case there was an error in one of our scans omitted from the successful mri_glmfit I re-ran the mri_glmfit/concatenation, excluding participants not also included in our successful mri_glmfit. However, the abnormal activation persisted (see attached screen grabs). I've also tried de-meaning our covariate of interest values (RBC Folate) and re-running the mri_glmfit, with no improvement.
This is our mri_glmfit command:
mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz
--fsgd /cluster/roffman/users/fsgd/GDD/137_GDD_Cond2vFix_Covary_RBC_Folate_linear_KDcorrect.fsgd
--C /cluster/roffman/users/fsgd/TwoGroups1CovariateRegressOut1Covariate_KD
--glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/2vFix_ClassUsed_Covary_RBCFOLATE_Nuis_Age_Gender
--fwhm 6 --no-prune
Thank you very much, I am most appreciative of your help and would be grateful for any other troubleshooting suggestions you might have!
Kind regards,
Kevin
Message: 2
Date: Mon, 5 Dec 2016 14:41:15 -0500
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Odd Extremely High/Low Banding of Functional
        Values in Volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 52df3c71-0cdc-61ba-2491-5bebffa114c1@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
How did you create sig.mgh? If you used a surface-based mri_glmfit
analysis, then you'll need to convert sig.mgh to the volume (mri_surf2vol)
On 12/05/2016 02:25 PM, Dowling, Kevin Francis wrote:
...
Hello Freesurfer Experts,
I?m attempting to look at activity in a working memory paradigm using
blood folate levels as my covariate of interest while controlling for
gender and age in 137 subjects. There were no errors (that I could
find) in the concatenation or mri_glmfit commands, and subject
registration looked ok for the functional data. When visualizing the
right and left hemisphere surface sig.mgh files using tksurfer
everything looks reasonable. However, when using tkmedit (tkmedit
fsaverage1 orig.mgz ?overlay sig.mgh ?fminmax 1.3 3.3 ?fmid 2.3) I am
getting odd continuous bands of incredibly high and incredibly low
activation spanning throughout most the volume (I?ve attached some
screen grabs ? the functional values in these bands are either
10000000000 or -10000000000 and look continuous from slice to slice).
I?ve taken a look at the list and was not able to find a similar
problem discussed. I would be most grateful for any guidance or
trouble shooting suggestions you might have!
I?ve also attached a text file copy of the glm and tkmedit results in
case they would be of use.
I'm using Freesurfer version 5.3 (nmr-stable53-env) on a Linux
(Release 6.7 (Santiago), Kernel Linux 2.6.32-573.12.1.el6.x86_64
and GNOME 2.28.2)
Thank you!
Kevin
Kevin Dowling
Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA, 02129
(p) (617) 643 - 2479

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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Kevin F. Dowling
Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA, 02129
(p) 617.643.2479