On 2/16/15 9:31 AM, Bruce Fischl wrote: > 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. This corresponds to the "cortex unknown" label in aparc (and is probably labeled WM in the aseg). This is normal. > > 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 > >
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