: 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
Thank you both! On Linux, 8GB is insufficient, and 16GB is normally
sufficient; I wonder if the requirements are a bit higher on MAC?
Could you please try the following?
1. Edit $FREESURFER_HOME/bin/segmentHA_T1.sh (might require sudo)
2. Replace the line:
set RESOLUTION="0.33
: 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
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
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
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
External Email - Use Caution
Dear Wu,
The “templates” are probabilistic atlases with no image intensities. All you
can look at is images like the ones in the top panel of Figure 5 in the paper.
If you want to generate these, let me know and I’ll show you instructions (it’s
a bit
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
: 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
External Email - Use Caution
Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing
Hi Alexis,
Yes please send me the images!
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of Alexis Guyot
Reply-To: Freesurfer support list
Date: Monday
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
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
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
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
.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
, 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
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
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
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 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 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 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
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
] 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
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
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
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
Hi Matt,
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 9 Jun 2016, at 19:31, Matt Glasser mailto:m...@ma-tea.com>>
wrote:
I would be intereste
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
I would be interested to know how well 0.7mm isotropic resolution data
performs at hippocampal segmentation. It would be better if folks could do
this then needing to acquire specialized anisotropic scans for hippocampal
segmentation.
Peace,
Matt.
From: on behalf of Fernando
Pasquini Santos
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
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
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
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