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. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > -- > > 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>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > 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 > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > 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