Dear Koen and Freesurfers, I haven't receive any further replies regarding the black lines surrounding the subfields I found in the sample of subjects I am analyzing.
As I said the subjects are quite young (9-14 years of age) and I visualized the subfields with Freeview. Do you have any idea why this is happening? This does mean the GEMS tool should not be applied in such young subjects? Any help would be greatly appreciated! Many thanks, joana 2014-06-13 15:40 GMT+02:00 Joana Braga Pereira <jbragapere...@gmail.com>: > Hi Koen, > > Thanks for such a prompt reply. > > I visualized it in freeview with: > > freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz > -p-labels posterior_right* posterior_Right-Hippocampus.mgz -p-prefix > posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt > > Thanks, > > Joana > > > 2014-06-13 15:23 GMT+02:00 Koen Van Leemput <k...@nmr.mgh.harvard.edu>: > > Hi Joana, >> >> This looks like a visualization issue rather than a segmentation error to >> me. How did you visualize this? >> >> Koen >> On Jun 13, 2014 2:59 PM, "Joana Braga Pereira" <jbragapere...@gmail.com> >> wrote: >> >>> Dear all, >>> >>> I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of >>> hippocampal subfields in subjects between 9 and 14 years of age with 3T >>> T1-weighted MRI scans. >>> >>> I noticed that a blackline is consistently drawn around the surface of >>> the subfields (see attached figure) and was wondering whether this is >>> normal. >>> >>> Since the tool has not been validated in young subjects I would like to >>> know if the black line observed in the figure shows that the segmentation >>> has not been carried out correctly. >>> >>> Any help will be greatly appreciated. >>> >>> Many thanks, >>> >>> Joana >>> >>> _______________________________________________ >>> 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. >>> >>> >> _______________________________________________ >> 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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