Yes, that is normal
On 2/16/15 11:42 AM, 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
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