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.
- 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?
- 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
- 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.
- 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.
- 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?
- 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
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Bruce Fischl