That red dot is fine. I bigger question is why you are using a 
development version from July 2016? The development versions are often 
unstable.


On 03/06/2017 05:27 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I looked at the medial wall area in lh.MEQ_area.10.mgh and noticed a 
> small cluster 'red' colored, please find it attached. Rest of the 
> brain surface is 'yellow'.
> I am not sure what can I interpret front his?
>
> Version I am using is: 
> freesurfer-Linux-centos6_x86_64-dev-20160701-61ad3a0
>
> Thanks.
>
> On Mon, Mar 6, 2017 at 2:31 PM, Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>     Hmm, something is going wrong because medial wall areas should
>     have been
>     masked out. Take a look at the medial wall area in lh.MEQ_area.10.mgh
>     file with something like
>
>     tksurferfv fsaverage lh inflated -aparc -ov lh.MEQ_area.10.mgh
>     -fminmax
>     .001 .1
>
>     scroll through the subjects to see if you see any non-zero signal
>     in the
>     medial wall
>
>
>     Are you using v6?
>
>
>     On 03/06/2017 04:26 PM, Martin Juneja wrote:
>     > Hi Dr. Greve,
>     >
>     > I am using following commands:
>     >
>     > recon-all -all -subject S01 -i T1w_S01.nii -qcache
>     > mris_preproc --fsgd MEQ.fsgd --target fsaverage --hemi lh --meas
>     area
>     > --out lh.MEQ_area.mgh
>     > mri_surf2surf --hemi lh --s fsaverage --sval lh.MEQ_area.mgh
>     --fwhm 10
>     > --cortex --tval lh.MEQ_area.10.mgh
>     > mri_glmfit --y lh.MEQ_area.10.mgh --fsgd MEQ.fsgd dods --C
>     > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
>     lh.MEQ_area.glmdir
>     > mri_glmfit-sim --glmdir lh.MEQ_area.glmdir --cache 1.3 neg --cwp
>     0.05
>     > --2spaces
>     > mri_glmfit-sim --glmdir lh.MEQ_area.glmdir --cache 1.3 pos --cwp
>     0.05
>     > --2spaces
>     >
>     > Thanks.
>     >
>     > On Mon, Mar 6, 2017 at 2:00 PM, Douglas N Greve
>     > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >     I think you might be doing something wrong during preprocessing.
>     >     Can you
>     >     send your command lines?
>     >
>     >
>     >     On 03/06/2017 12:11 PM, Martin Juneja wrote:
>     >     > Hello experts,
>     >     >
>     >     > I am trying to correlate cortical surface area measure with
>     >     behavioral
>     >     > measures using instructions from here:
>     >     >
>     >
>     https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>     <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
>     >   
>      <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>     <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>
>     >     >
>     >   
>      <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>     <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
>     >   
>      <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>     <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>>
>     >     >
>     >     > After I overlay pcc.mgh (partial correlations) and sig.mgh
>     files on
>     >     > lh.inflated, I see some clusters with high PCC values
>     (Destrieux
>     >     > atlas) (please see attached figure) at "unlabeled subcortical
>     >     regions"
>     >     > for one of the behavioral measures, out of 4.
>     >     >
>     >     > Although for volume and thickness versus any behavioral
>     >     measures, I do
>     >     > not see any "unlabeled subcortical regions" clusters like
>     this.
>     >     >
>     >     > Could you please advise me if its normal to get these
>     clusters?
>     >     If so,
>     >     > how can I interpret that?
>     >     >
>     >     > Or Am I doing something wrong during preprocessing? If so, any
>     >     help to
>     >     > find out where I might be doing wrong and to fix the issue
>     would be
>     >     > really appreciated.
>     >     >
>     >     > Thanks.
>     >     >
>     >     >
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>     >     --
>     >     Douglas N. Greve, Ph.D.
>     >     MGH-NMR Center
>     > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     gr...@nmr.mgh.harvard.edu <mailto:gr...@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
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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