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

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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