Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Joshua Ezequiel Pasaye]

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Dear Dr. Iglesias,

Thank you for your quick response and insight. I wanted to make sure that there 
were not any specific requirements for the T2w scan when using the segmentation 
command. I will try both and let you know my thoughts.

Kindly,


Joshua E. Pasaye, B.S. (he/him/his)
Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
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 amygdala
Dear Joshua,
This is a bit of an empirical question. I’d totally run both on a few subjects 
and compare the results.
If you do so: I would selfishly/greatly appreciate it if you shared your 
impressions with me :-)
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1AgZJS_lt0DLao4RNJQjdUp6--s94lZQRuhY7Nebh6-r-KlmJo3_XFlRC0kfAa6vzJjeVQXzkeeaH7zelX9kI_IrS8lXLH0j_1vVxwTtbuFhkTFdoSyhIVu89ibzpZeN4YjLlV8qw7HSRnWeTxN16KatsH0eVYzaGfg6bTsLJZ0P773bRtcTT2UTUolqQD8FXD14dl_UyS3EbkyswIGDv8P3j3JOh17S3AoTqZiZWc54POqnTkqUThnCFaD3LiJWA3qzkZHpOzNDR8uKXd0labEq8IuK2ZdP7fS454aGeXwWtqjdKTm9QX_vNEkCTpQQx/http%3A%2F%2Fwww.jeiglesias.com

From: 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

External Email - Use Caution
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 Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w 
SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes 
Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated 
MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to 
run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  
USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal 
sequence so to compare the two outputs, it would be ideal to also use the 
HighRes Hippocampal sequence.



Please let me know if you need additional information.



Thanks,


Joshua E. Pasaye, B.S. (he/him/his)
Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Iglesias Gonzalez, Juan E.]

Dear Joshua,
This is a bit of an empirical question. I’d totally run both on a few subjects 
and compare the results.
If you do so: I would selfishly/greatly appreciate it if you shared your 
impressions with me :-)
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: 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

External Email - Use Caution
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 Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w 
SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes 
Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated 
MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to 
run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  
USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal 
sequence so to compare the two outputs, it would be ideal to also use the 
HighRes Hippocampal sequence.



Please let me know if you need additional information.



Thanks,


Joshua E. Pasaye, B.S. (he/him/his)
​Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu
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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Joshua Ezequiel Pasaye]

External Email - Use Caution

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 Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w 
SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes 
Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated 
MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to 
run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  
USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal 
sequence so to compare the two outputs, it would be ideal to also use the 
HighRes Hippocampal sequence.



Please let me know if you need additional information.



Thanks,


Joshua E. Pasaye, B.S. (he/him/his)
​Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu
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continue communication over unencrypted e-mail, please notify the sender of 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Yes! The changes will probably be tiny, though.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Boris Rauchmann 

Reply-To: Freesurfer support list 
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 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 not sure if I also have to rerun the subfields pipeline now?

Thanks,
Boris

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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Boris Rauchmann]

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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 not sure if I also have to rerun the subfields pipeline now?

Thanks, 
Boris

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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Meena M. Makary]

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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 which exists in the development version
of 2018 but not in vr 6.0. I copied this bash file and other related files
from the development version to my vr 6.0 /freesurfer/bin directory but I
stuck with errors related to the MATLAB runtime version (it needs MCRv84).
I downloaded runtime2014bLinux (MCRv84), but still same errors. Any
recommendation to overcome this problem?.
Will it be okay if I just replaced my vr6.0 /freesurfer/bin folder by the
one from the recent development version? - given that I analyzed my data
using recon-all by vr6.0.

Thanks;
--Meena

-- 

*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University 
Postdoctoral Fellow | Yale University School of Medicine

Postdoctoral Associate |  The John B. Pierce Laboratory

Treasurer | OHBM Student and Postdoc SIG


290 Congress Avenue, New Haven, CT 06519
+1 (475) 731-5592 <+1%20475-731-5592>
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Carme Uribe Codesal]

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,
>
> 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 advance!
>
> Carme Uribe
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[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,

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 advance!

Carme Uribe
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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Carme Uribe Codesal]

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 advance!

Carme Uribe
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