Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there.
2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: > Hi experts, > I'm rather unexperienced with freesurfer so please excuse my basic > requests. > 1. I controlled the segmentation of the entorhinal cortex (EC) in over > 50 subjects following the borders described in Fischl 2009 (Predicting > the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg > aparc-aseg.mgz. > I noticed (esp. in the coronar slices and in approximately every mri) > brain tissue between amygdala/ hippocampus/ temporalpole and the EC > labelled as "none" or "ctx-?h-unknown". Has anything gone wrong with the > segmentation? Or is a label (e.g. perirhinal cortex) not loaded? > > 2. Is there a possibility to visualize the EC volume in freeview or > tkmedit from the exvivo.stats or exvivo.label file? I would like to > compare it to the other EC volume because they have very different > volumes. In the mail archive were similar questions about that but you > haven't answered them yet. > > Many thanks in advance, > Melina > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 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.
