On Mon, Mar 6, 2017 at 2:31 PM, Douglas N Greve <greve@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

> <greve@nmr.mgh.harvard.edu <mailto:greve@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>>
> >
> > 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
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--
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
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