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
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
>
> 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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