Hi Joana, Sorry for the delayed response. I'm a bit puzzled because it really looks like a visualization issue in freeview. Could you please send me the original *.mgz files, so I can try the visualization myself?
Thanks, Koen On Mon, Jun 23, 2014 at 9:38 PM, Joana Braga Pereira <jbragapere...@gmail.com> wrote: > 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. >>> >> > > > _______________________________________________ > 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
