n.edu<mailto:joshua.pas...@northwestern.edu>
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Date: Friday, November 17, 2023 at 2:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of
the am
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Joshua Ezequiel Pasaye
Date: Friday, November 17, 2023 at 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the
amygdala
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Hello,
I am working
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Hello,
I am working on project using Freesurfer’s “Segmentation of hippocampal
subfields and nuclei of the amygdala” to segment the hippocampal subfields and
compare it with a software called ASHS developed by the Penn Image Computing
and Science L
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Thanks!!!
Kind regards,
Rosie
El mié., 7 jul. 2021 21:32, Paul Wighton escribió:
> External Email - Use Caution
>
> Hi Rosie,
>
> In that case, you can try running the v6 version of hippocampal subfields,
> e.g:
>
> recon-all -s sub-002_ses-
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Hi Rosie,
In that case, you can try running the v6 version of hippocampal subfields,
e.g:
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
-Paul
On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo
wrote:
> External Email - Use Caut
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Hi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I
made some corrections (control points,...). I just want the hipocampal
subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul
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Thanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is
not in this version.
There are two options. If you want to continue using v6.0.0, you can
refer to the instructions here:
https://secure-web.cis
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Here it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la
$FREESURFER_HOME/bin/segmentHA_T1.sh
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file
or directory
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-st
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Ok, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't
exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/frees
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Hi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh
$ segmentHA_T1.sh
sh: 1: segmentHA_T1.sh: not found
$
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani wrote:
> External Email - Use Caution
>
> Dear Rosalia,
>
> Once y
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Dear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh
after sourcing and then try running it(without closing the terminal)
hopef
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Hi Paul,
I did it:
# FREESURFER
export FREESURFER_HOME=/usr/local/freesurfer
export PATH=${FREESURFER_HOME}/bin:${PATH}
export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI
source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer b
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Sure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come
after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows,
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Hi Paul,
Thank you very much for answering my question. I set the subjects_dir in a
way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME
/usr/local/freesurfer
rosali
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Hi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin
directory. It looks like your PATH environment variable does not include
this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo
$FREESURFER_H
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Following this more actualized link:
https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoT
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Dear Freesurfer team,
Following this link:
https://secure-web.cisco.com/1JQvIqqm3-q4IvkVi2SEZWuHP3qoo3qga0SfN71vLNIZ9qj4cNFwxFqvjroWv9feMAvJHN9UgN0BkjDoYeCHTilHRlhYVCx9NC7MYk-9O0bZVNfhvJz8OO5I1ewNoWK_GpUl2x9NzWTare9e3GblcaHIpBuMhXHYKv_uZ0aA0f7RFNcL2xlX
Date: Wednesday, 5 June 2019 at 15:12
To: Freesurfer support list
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the
amygdala
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Dear all,
depends the Segmentation of hippocampal subfields and nuclei of the amygdala
pipeline on the
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Dear all,
depends the Segmentation of hippocampal subfields and nuclei of the amygdala
pipeline on the fs-recon all pipeline? I made some changes mainly by defining
control points to fix intensity normalization in my dataset and rerun recon
all. I´m
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Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module
on the 6.0-reconned data.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
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Dear FreeSurfer experts,
we would like to use the 'Segmentation of hippocampal subfields and nuclei of
the amygdala' feature [1] that is available in the development version of
FreeSurfer.
However, we already pre-processed all subjects from the stu
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Hi;
My Linux machine has FreeSurfer 6.0 with MATLAB runtime2012bLinux (MCRv80)
which allows me to do the hippocampal subfields segmentation without
errors. Now, I'd like to use [segmentHA_T1.sh] for hippocampal and
nuclei of the amygdala segmentation w
Great! Thanks!
2018-01-08 16:44 GMT+01:00 Hoopes, Andrew :
> Hi Carme,
>
> segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh.
> harvard.edu/pub/dist/freesurfer/dev
>
> best,
> Andrew
>
>
> On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal
> wrote:
>
> Dear FreeSurfer users,
Hi Carme,
segmentHA_T1.sh is available in the fs dev version:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev
best,
Andrew
On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal
mailto:carme.ur...@gmail.com>> wrote:
Dear FreeSurfer users,
I wanted to run the new script that segments the h
Dear FreeSurfer users,
I wanted to run the new script that segments the hippocampus and
amygdala (segmentHA_T1.sh:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
but I can't find it in FreeSurfer 6.0. Is it already available?
Where can I find it?
Thanks in adv
Hi Stefano
FS version 6 is not ready yet - it's still in testing. Hopefully we will
have a beta for people to tryout soon
Bruce
On Fri, 15 May 2015, std...@virgilio.it wrote:
hi list,
where can I download the new version 6.0 of hippocampal subfields
segmentation? And in general the new FS
hi list,
where can I download the new version 6.0 of hippocampal subfields segmentation?
And in general the new FS version 6.0?
Thanks
Stefano
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>
>
> - Original Message -
> From: "Josh Gray"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Monday, May 11, 2015 1:33:32 PM
> Subject: [Freesurfer] Segmentation of hippocampal subfields / version 6.0
> release d
- Original Message -
From: "Josh Gray"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, May 11, 2015 1:33:32 PM
Subject: [Freesurfer] Segmentation of hippocampal subfields / version 6.0
release date
Hello,
I wanted to inquire about when you think that this new p
Hello,
I wanted to inquire about when you think that this new package for
freesurfer 6.0 will be complete? I am interested in pursuing hippocampal
segmentation, but it seems that I should not use the segmentation from your
older program and I should wait, would you agree?
Thank you,
Josh
--
Jo
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