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. > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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> 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> . 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer