PONTICORVO
Reply-To: Freesurfer support list
Date: Thursday, April 8, 2021 at 03:22
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] thalamic nuclei segmentation
External Email - Use Caution
Hi Freesurfer experts,
I processed ~150 subjects with freesurfer v6 (recon-
External Email - Use Caution
Hi Freesurfer experts,
I processed ~150 subjects with freesurfer v6 (recon-all) and I was
wondering if it is possible to use the script for the segmentation of the
thalamic nuclei on these subjects.
I know this part of the processing is now integrated
Thanks, Franziska.
It seems to be a problem with partial voluming. Cerebral white matter (white
pixels) mixes with a thin layer of cerebrospinal fluid (black pixels) and the
result is a bunch of gray pixels that look like the pulvinar.
Partial voluming is one of the biggest problems with these
External Email - Use Caution
Dear Eugenio,
here are the zipped norm.mgz and automated segmentations for two subjects:
ar Eugenio,
do you mean the "ThalamicNuclei.v12.T1.mgz" files?
Best regards,
Franziska
___
Date: Thu, 11 Mar 2021 16:29:45 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Thalamic nuclei segmentation -
External Email - Use Caution
Dear Eugenio,
do you mean the "ThalamicNuclei.v12.T1.mgz" files?
Best regards,
Franziska
___
Date: Thu, 11 Mar 2021 16:29:45 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Thalamic
Dear Franziska,
Can you please send the automated segmentations as well?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On 3/11/21, 09:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Gronow,
External Email - Use Caution
Here are the norm.mgz files of two subjects as .zip file:
mgh.harvard.edu'"
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus
mis-segmentation?
External Email - Use Caution
Dear Eugenio,
thanks for your response. I wasn’t sure whether .mgz files contain patient
information so I had to clarify that. It would be great if yo
. Can I send them directly via email or do you prefer dropbox?
Thanks again!
Best regards, Franziska
--
Message: 17
Date: Tue, 23 Feb 2021 16:20:43 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nu
V0gQJ81Vnbun-w1jgpS-nfAm_-xzKpU5Ahvz3D6YuiiBxYVQnnu9El0ohZ5YagIdqXdrc43RZCrThc2UylfmrcEP886ol_DPKenpIizoowtawtzz6jO51KKU2At0huy5rSrNZVc1NMkBOVtnBiLJO4aMh4DTDzbg8Wyv80_vcz45LmZe01n8g/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210216%2Fd3f31b14%2Fattachment-0001.html
Kw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F
> mailman%2Flistinfo%2Ffreesurfer
-- next part --
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1JvBfmBi57GPnae3pffFHMt7spN6t92V5q1T0KcXFfz112mLbY18bi4zNYqaR1fDllzuPRzvHPPZdhJsFy_-JS_5TYCypyTd1DV0gQJ81Vnbun-
Freesurfer support list
Date: Wednesday, February 17, 2021 at 08:54
To: Freesurfer support list
Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus
mis-segmentation?
Dear Franciska,
It’s hard to tell from a single plane, but it seems that dark voxels from the
ventricles
.edu'"
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus
mis-segmentation?
External Email - Use Caution
Dear Freesurfer experts,
I’ve been using Freesurfer 7 for only a few months. I've searched the list and
no similar observations have been reported.
For my project I us
External Email - Use Caution
Dear Freesurfer experts,
I've been using Freesurfer 7 for only a few months. I've searched the list and
no similar observations have been reported.
For my project I used the "Segmentation of thalamic nuclei" tool by Iglesias,
J.E. et al.
The
It will ignore the projmap option, so you can just leave it as X (it can
be any string, but there does have to be something there). For the reg,
use regheader
On 6/4/2020 6:00 AM, Quentin Devignes wrote:
External Email - Use Caution
Dear Doctor Greve,
Thank you for your reply. I
External Email - Use Caution
Dear Doctor Greve,
Thank you for your reply. I am trying to do what you advised me.
For now, I have segmented thalamic nuclei in the left hemisphere, checked and
corrected this segmentation and used MRI_binarize as advised. However, I don’t
know
://www.jeiglesias.com
From: on behalf of Miguel Ángel Rivas
Fernández
Reply-To: Freesurfer support list
Date: Sunday, 8 December 2019 at 15:00
To: Freesurfer support list
Subject: [Freesurfer] Thalamic nuclei segmentation
segmentThalamicNuclei.sh 4001
/Applications/freesurfer_dev/freesurfer
External Email - Use Caution
Dear Freesurfer devs,
I tried to run the thalamic nuclei segmentation (T1 and T2 as input) using
the freesurfer dev version and the terminal gave to me the following error
rmnlab1:~ neucoga$ segmentThalamicNuclei.sh 4001
Sent: Wednesday, March 27, 2019 3:09:21 AM
To: Freesurfer support list
Subject: [Freesurfer] Thalamic nuclei segmentation
External Email - Use Caution
Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version.
However, when I input "freeview -v nu.m
External Email - Use Caution
Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version.
However, when I input "freeview -v nu.mgz -v
ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview,
just nu.mgz. What's the matter? Please
http://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei
On 2/14/19 2:21 PM, Antti Cajanus wrote:
> External Email - Use Caution
>
> Hi!
>
> Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer
> development version and I had it working fine. However, I can’t find
External Email - Use Caution
Hi!
Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer
development version and I had it working fine. However, I can’t find the web
page anymore with the instructions how to use the tool. Is the tool still in
use and if so,
: [Freesurfer] Thalamic Nuclei segmentation results
External Email - Use Caution
Dear all,
I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the results
of segmentation appear to be very poor, i am annexing the results , please
kindly review if there is any thing wrong
External Email - Use Caution
Dear all,
I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the
results of segmentation appear to be very poor, i am annexing the results ,
please kindly review if there is any thing wrong with the segmentation
results.
Thanks
External Email - Use Caution
Hi Freesurfer devs,
Just a simple question, it´s possible make the thalamic nuclei segmentation
using as input a simple T2 image as additional scan or by contrary, is
always required use as input a more specific scan such as the FGATIR or a
DBS scan.
26 matches
Mail list logo
