Hello FreeSurfer Developers,
I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
Hello FreeSurfer Experts,
I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
Dear Koen & Freesurfers,
I've been working with the GEMS tool for hippocampal subfields
segmentation and have a question I would like to ask you all.
I've noticed that the CA1 sector appears to be quite small compared to
other subfields (CA2-3 seems to be the largest), while previous
studie
Dear Freesurfer developers,
I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the
hippocampal subfields of two 7T MR images in NIFTI format: an isotropic
(0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic
(0.3*1.2*0.3 mm3) T2-weighted volume covering
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Hello Freesurfer users,
I was wondering if there is any Freesurfer code available for performing
hippocampal subfield segmentation on multiple subjects simultaneously in
parallel. I already have the code for analyzing a single subject, but I'm
intere
Hello,
I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some
library (libmwi18n.so for example, it was missing others before that
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 27 J
I tried that. but didn't work.
Cheers,
Pierre
On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio
wrote:
> Hi everyone,
> you need to install the Matlab 2012b runtime as explained in the wiki:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
>
>
>
> Juan Eugenio Igle
Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out
what’s going on. But it definitely sounds funny that it is asking for the CTF,
since this is supposed to be embedded in the executable… I’ll get back to you
as soon as possible.
Cheers,
Eugenio
Juan Euge
I could finally look into this. It is indeed weird. The CTF is indeed embedded
in the executable…
Zeke/Nick, can you shed some light on this?
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 27
Hi,
I still have a problem as well with the subfields segmentation (ubuntu
14.04, with the files .ctf)
Cheers,
Pierre
Hello FreeSurfer Experts,
I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesu
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of pierre deman
Sent: Tuesday, July 5, 2016 7:04:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation
Hi,
I still have a problem as well with the subfields segmentation (ubuntu 14.04,
with the files
Dear Freesurfer Developers,
For my research I'm trying to run the hippocampal subfield segmentation
analysis however, I keep running into the following error. I tried to solve it
by myself however I had no luck ( I tried by removing the exec flag from the
files ).
I'm using the following sofft
Hi Joana,
The smallness of our CA1 compared to other protocols seems to be
caused by disagreements in the fields of where the subfield boundaries
should be located. I've talked to several experts on this and they all
are confident that their own definition is the only "right" one. :-)
As for the
Dear Koen,
Thanks! I will wait for Dr. Augustinack and Dr. Dickerson's answers.
joana
2012/1/26 Koen Van Leemput
> Hi Joana,
>
> The smallness of our CA1 compared to other protocols seems to be
> caused by disagreements in the fields of where the subfield boundaries
> should be located. I've t
I am not an expert but I'll say this as far as compliance to Duvernoy: In
the body of the hippocampus, compliance to Duvernoy is quite strongmuch
better than any others I've seen. However, according to my reading of
Duvernoy, the positions of the subfields change in the anterior head and
poster
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Hello,
I am running segmentation of hippocampal subfields in FreeSurfer 6.0 but
one subject failed running the segmentation with the following error
message.
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does n
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Dear FS developers,
I uesd the ''recon-all command'' to get the volumes of the hippocampal
subfields, and we would like to perform further analysis with these subfields
in MNI. Could you show us the templates which are used to perform hippocampal
: Monday, 22 January 2018 at 17:49
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Hippocampal subfields segmentation
Dear Freesurfer developers,
I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the
hippocampal subfields of two 7T MR images in NIFTI
External Email - Use Caution
Hello, freesurfer experts
I'm trying to run segmentation of hippocampal subfields and nuclei of
amygdala by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and
license, as well as the required matlab
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine
running on Windows 10?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 24
nstall ...
Sincerely,
Michel hu
Van: freesurfer-boun...@nmr.mgh.harvard.edu
namens Iglesias Gonzalez, Eugenio
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
Dear
ens Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine
running o
du>>
namens Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virt
April 2019 at 04:38
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Hippocampal subfields segmentation template
External Email - Use Caution
Dear FS developers,
I uesd the ''recon-all command'' to get the volumes of the hippocampal
subfields, and we
Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of 오진영
Reply-To: Freesurfer support list
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu"
Cc: JongHyun Lee
Subject: [Freesurfer] hippocampal
: Freesurfer support list
Date: Monday, 30 July 2018 at 09:29
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields segmentation error
External Email - Use Caution
Dear Eugenio,
Thanks for your reply.
I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2b
http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list
> *Date: *Monday, 30 July 2018 at 09:29
> *To: *Freesurfer support list
> *Su
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Hi,
I am also encountering the same issue as WON JONG CHWA on my macbook pro (16gb
ram) and I even tried the same on imac (8gb ram). I ran recon-all successfully
on both systems. Here are my system details
Hardware Overview:
Model Name: MacBook
External Email - Use Caution
I”m wondering if this is an issue with the version of Java installed on the
machine and Matlab. I’ve seen the latest MCR Matlab installer try to make
changes to java installed on a Mac. So maybe updating or re-installing
the Matlab software on your
Cc: Ramtilak Gattu
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
[EXTERNAL]
I”m wondering if this is an issue with the version of Java installed on the
machine and Matlab. I’ve seen the latest MCR Matlab installer try to make
changes to java installed on a Mac. S
ay.com>Sent: Tuesday, March 23, 2021 11:00
PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Ramtilak
Gattu <rg...@med.wayne.edu>Subject: Re: [Freesurfer] Hippocampal
Subfields Segmentation Violation-error [EXTERNAL]I”m wondering if this is
an issue with the version of
: Ramtilak Gattu
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
Maybe you could let us know if the system integrity protection feature is
turned on the Mac (which is the default). The following command will report if
it is enabled or disabled, e.g., when enabled
Reply-To: Freesurfer support list
Date: Tuesday, March 23, 2021 at 17:46
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
External Email - Use Caution
External Email - Use Caution
Hi,
I am also encountering the
: fsbuild , freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
External Email - Use Caution
External Email - Use Caution
Hi 'E' / 'R',
I even tried changing the resolution to 1.0 with no success rulin
Dear,
I have a doubt regarding the input T1 image used for the Hippocampal
Subfield segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
In this documentation it says that I can use a standard 1mm T1 image or the
same standard 1mm T1 image with an additi
Reply-To: Freesurfer support list
Date: Thursday, June 9, 2016 at 1:23 PM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?
Dear,
I have a doubt regarding the input T1 image used for the Hippocampa
Hi Fernando,
Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to
take advantage of multiple images with higher resolution, but it hasn’t been
thoroughly tested and it’s not publicly availa
;
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel
size of the input?
Dear,
I have a doubt regarding the input T1 image used for the Hippocampal Subfield
segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/
er support list
Date: Thursday, June 9, 2016 at 1:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?
Hi Matt,
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio
Juan Eugenio Iglesias
Translation
genio
[e.igles...@ucl.ac.uk]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?
Hi Fernando,
Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code
assu
boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Iglesias, Eugenio
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation
] on behalf of Iglesias, Eugenio [
> e.igles...@ucl.ac.uk]
> *Sent:* Thursday, June 09, 2016 2:36 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Hippocampal subfields segmentation - what is
> the voxel size of the input?
>
> Hi Fernando,
>
> Unfortunately
, Eugenio
[e.igles...@ucl.ac.uk]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?
Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t
crash when you run
.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Iglesias, Eugenio
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of th
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