Hi Melina Sorry for the delay in responindg, can you tell us a bit more about the acquisition? They look very grainy and low contrast.
Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: > Thank you both for your respond. > 1. I have attached you some pictures. Like douglas wrote it corresponds to > white matter in aseg, but is more often labelled as "none" than "cortex > unknown". So is this "normal" and can I trust those borders? Or would you > rather advise to control aseg and aparc segmentation to estimate the > entorhinal cortex segmentation? > > 2. You're right, Bruce, in freeview the exvivo label it just follows the > surface. So I'll try mri_label2vol. > > Cheers Melina > > Am 16.02.2015 um 16:33 schrieb Douglas Greve: >> 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 >>> >>> >> _______________________________________________ >> 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
