you can
mri_binarize --match 1006 --i aparc+aseg.mgz --o left.entorhinal.mgz
(use 2006 for right).
These values you can get from $FREESURFER_HOME/FreeSurferColorLUT.txt
On 5/24/17 9:57 AM, Stephanos Leandrou wrote:
Dear Freesurfer Developers,
I want to extract the entorhinal cortex from the
Dear Freesurfer Developers,
I want to extract the entorhinal cortex from the original T1 image of my
subect's MRI scans. Is there a way to do it; I used the the commands below to
extract the CA1 subfield of the hippocampus. Is there a similar way to do the
same for the entorhinal cortex?
mri_
use 1006
On 02/06/2017 08:33 AM, std...@virgilio.it wrote:
> Hi list,
> for entorhinal and perirhional cortices in FS-FAST should I use 1006
> ctx-lh-entorhinal or 216 entorhinal_cortex?
> Thanks
>
> Stefano
>
>
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Hi list,for entorhinal and perirhional cortices in FS-FAST should I use 1006
ctx-lh-entorhinal or 216 entorhinal_cortex?Thanks
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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
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
tho
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
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 yo
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.mg
Hi list,
I have read the article on EC (Neuroimage).
But, I do not understand how I should obtain the EC thickness outcomes
/statistical maps from my analysis.
I have some question, please.
I have already performed recon-all and cortical thickness analysis.
For entorhinal cortex thickness analysi
Thanks for quick response Bruce. We will use the volume from ex-vivo
stats..
Regarding the need to integrate the ex vivo one back into aparc+aseg.
We noticed the entorhinal volume in aparc is larger than that in
exvivo.stats.
So do the extra entorhinal voxels in aparc need to be re-labelled as
"
Hi Mehul
the entorhinal label in the aparc was drawn by Rahul based on gyral
landmarks. The one in the _exvivo.stats is based on being able to see the
layer II islands in ex vivo MRI and hence we believe it is more accurate.
Not sure why you need to integrate the ex vivo one back into the
apa
Hi Folks,
I have a question about entorhinal cortex volume. The entorhinal cortex is
listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous
post on the mailing list, it was mentioned that we should use the volume
measurement from ?h.entorhinal_exvivo.stats.
We would like to make
Hi Imagers:
Is there a command that will allow you to extract the volumes of the
EC from the Entorhinal Ex vivo label ? I need to extract this in 77
brain scans.
thanks ~
Alan
BIDMC/ Boston
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ht
Hi: I understand that information on the accuracy of the entorhinal cortex
parcellation, for each subject, may be found in their
?h.entorhinal_exvivo.label file. I reviewed this file but could not tell which
column (if any) contains accuracy information. Could someone point me in the
right dire
Another basic question:
Could you tell me what is the best way of putting the
?h.entorhinal_exvivo.stats into a spreadsheet for all subjects? Is there a way
to achieve a textfile output for all subjects similar in concept to
kvlQuantifyHippocampalSubfieldSegmentations.sh ?
catherine_
Hi Catherine
I guess I would recommend the ex vivo one since it is based explicitly on
architecontics and not on guessing locations from folds.
cheers
Bruce
On Wed, 7 Dec 2011, Cat Chong wrote:
Hello experts,
I am very new to freesurfer so please excuse my basic question:
We want to get
Hello experts,
I am very new to freesurfer so please excuse my basic question:
We want to get measurements of entorhinal cortex volumes on a group of people.
I found these results listed in ?h.aparc.stats.
I also noticed another ?h.entorhinal_exvivo.stats, with different results.
Which shou
Hi Christine
does it look ok in the aseg?
Bruce
On Wed, 30 Nov 2011, Christine Smith wrote:
> Hello,
>
> I have a subject whose entorhinal cortex on one side of the brain is
> being excluded from the white matter surface and the pial surface. The
> cortex is included in the brain mask.
>
> I hav
Hello,
I have a subject whose entorhinal cortex on one side of the brain is
being excluded from the white matter surface and the pial surface. The
cortex is included in the brain mask.
I have tried a number of approaches to fix the problem but none have
worked. First, I set some control points in
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