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> 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> > > > > 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. > > > > > > _______________________________________________ > > 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 > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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