Re: [Freesurfer] Brainstem segmentation without pre-processing

2023-12-28 Thread Iglesias Gonzalez, Juan E. 
Dear Ali,
Making a SynthSeg version of the tool is on the to-do list but has not happened 
yet. For now, you need to run recon-all. The good news is that you get a ton of 
additional useful information on the brains!
Kind regards,
/Eugenio

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ganjizadeh, Ali, M.D. 

Date: Wednesday, December 27, 2023 at 22:04
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Brainstem segmentation without pre-processing

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Good evening,
I am trying to work with segmentBS.sh. I want to pass my .nii.gz files that are 
already pre-processed with HD-BET, but I don't want to use recon-all as the 
first step because it takes a lot of time. I also tried recon-all -autorecon2 
and 3, but it resulted in an error.

Is there any specific command that I will be able to pass my files directly to 
segmentBS.sh? Or is there any command for recon-all to only make subjects 
without processing or fast processing?

Thank you,
Ali


Ali Ganjizadeh, M.D. (he/him)

Postdoctoral Research Fellow

Mayo AI Lab (Radiology Information Lab)

Mayo Clinic-Rochester
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[Freesurfer] Brainstem segmentation without pre-processing

2023-12-27 Thread Ganjizadeh, Ali, M.D. 
External Email - Use Caution

Good evening,
I am trying to work with segmentBS.sh. I want to pass my .nii.gz files that are 
already pre-processed with HD-BET, but I don't want to use recon-all as the 
first step because it takes a lot of time. I also tried recon-all -autorecon2 
and 3, but it resulted in an error.

Is there any specific command that I will be able to pass my files directly to 
segmentBS.sh? Or is there any command for recon-all to only make subjects 
without processing or fast processing?

Thank you,
Ali


Ali Ganjizadeh, M.D. (he/him)

Postdoctoral Research Fellow

Mayo AI Lab (Radiology Information Lab)

Mayo Clinic-Rochester
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Re: [Freesurfer] Brainstem segmentation

2021-09-23 Thread Erik O'Hanlon 
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Dear Eugenio,

Thanks so much for your reply. I will certainly follow your instructions on 
"small volume" registration. That will certainly allow us to benefit from the 
more specialized volume showing neuromelanin within the LC area in conjunction 
with the whole brain T1 and brainstem component.

Very much appreciated

Best regards

Erik






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Thursday 23 September 2021 03:27
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brainstem segmentation

Dear Erik,

I never put together a multi-spectral version of the brainstem segmentation 
because, given the coarse structures that we segment (midbrain, pons, medulla, 
scp), there’s pretty much nothing to be gained from additional contrasts.

In terms of registration: if your “small volume” is acquired during the same 
session as the 1mm T1 you’ve processed with FreeSurfer, they should be almost 
overlapping in RAS coordinates. You can then use mri_robust_register with the 
—noinit flag to register the volumes. I would strongly encourage you to use the 
small volume as target of the registration and the 1mm T1 as source; you can 
always invert the resulting rigid transform matrix to go in the other direction.

Cheers,

/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1utF6ii16FKVLSJtWVYU_QqP1mwtxTj9C4VzTH0TRLK0acGF8EMLbdFaa8Dv_159f-HS2e-xguAL8vJmmD2VOC4slo1o-a6ZCZtFDMcEKgC_T_QAMj73Xew1zhJund5MNGcWTs7ADio9g4zzJv7DZXaAzNPvwJo2QHoo6c-L5tKD9r9TYrOvElG4-wm585jaBTDh_iuTOL60mLjxf-tjaC2Y7ZyRSgjEQyYnzMYJhAZw1Y70cho9-SxLgPeWpesRGZp0h4bUwIoOGTfjh-YarDA/http%3A%2F%2Fwww.jeiglesias.com

On Sep 20, 2021, at 18:43, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

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Dear Experts,

We hope to acquire some multishell dwi and structural data to investigate 
tracts passing through the Locus Coeruleus (LC) and we want to apply the 
brainstem segmentation to our structural data to obtain subject specific LC 
masks.
Is it possible to feed multispectral data into the brainstem segmentation ?
Is it possible to acquire a high res volume capturing the LC in greater detail 
and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in 
the delineation of the LC roi and quantification of the LC volume?
If it's possible to use an additional small volume like this, do I need to 
pre-process it using recon-all and what is the optimal way to co-register the 
small volume to the whole brain T1 to assist in the mask generation?

Any guidance is very much appreciated.

Best regards and thanks,

Erik




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Re: [Freesurfer] Brainstem segmentation

2021-09-22 Thread Iglesias Gonzalez, Juan E. 
Dear Erik,

I never put together a multi-spectral version of the brainstem segmentation 
because, given the coarse structures that we segment (midbrain, pons, medulla, 
scp), there’s pretty much nothing to be gained from additional contrasts.

In terms of registration: if your “small volume” is acquired during the same 
session as the 1mm T1 you’ve processed with FreeSurfer, they should be almost 
overlapping in RAS coordinates. You can then use mri_robust_register with the 
—noinit flag to register the volumes. I would strongly encourage you to use the 
small volume as target of the registration and the 1mm T1 as source; you can 
always invert the resulting rigid transform matrix to go in the other direction.

Cheers,

/Eugenio

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

On Sep 20, 2021, at 18:43, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

External Email - Use Caution

External Email - Use Caution

Dear Experts,

We hope to acquire some multishell dwi and structural data to investigate 
tracts passing through the Locus Coeruleus (LC) and we want to apply the 
brainstem segmentation to our structural data to obtain subject specific LC 
masks.
Is it possible to feed multispectral data into the brainstem segmentation ?
Is it possible to acquire a high res volume capturing the LC in greater detail 
and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in 
the delineation of the LC roi and quantification of the LC volume?
If it's possible to use an additional small volume like this, do I need to 
pre-process it using recon-all and what is the optimal way to co-register the 
small volume to the whole brain T1 to assist in the mask generation?

Any guidance is very much appreciated.

Best regards and thanks,

Erik




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[Freesurfer] Brainstem segmentation

2021-09-20 Thread Erik O'Hanlon 
External Email - Use Caution

Dear Experts,

We hope to acquire some multishell dwi and structural data to investigate 
tracts passing through the Locus Coeruleus (LC) and we want to apply the 
brainstem segmentation to our structural data to obtain subject specific LC 
masks.
Is it possible to feed multispectral data into the brainstem segmentation ?
Is it possible to acquire a high res volume capturing the LC in greater detail 
and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in 
the delineation of the LC roi and quantification of the LC volume?
If it's possible to use an additional small volume like this, do I need to 
pre-process it using recon-all and what is the optimal way to co-register the 
small volume to the whole brain T1 to assist in the mask generation?

Any guidance is very much appreciated.

Best regards and thanks,

Erik




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Re: [Freesurfer] Brainstem segmentation

2016-05-04 Thread Eugenio Iglesias 
Dear Haque, 
FreeSurfer 6 has not been released yet. But if you want to try the brainstem 
segmentation module, you can download the dev version; you will find it in 
there. 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Haque, Muhammad E" <muhammad.e.ha...@uth.tmc.edu> 
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 
Sent: Monday, May 2, 2016 5:24:48 PM 
Subject: [Freesurfer] Brainstem segmentation 



Dear FreeSurfer Users, 



I would like to know if we can do brainstem segmentation as described in the 
recent publication 

http://www.sciencedirect.com/science/article/pii/S1053811915001895 




Author as well as FreeSurfer website mention that this feature is only 
available in FreeSurfer 6.0 and later version 



https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures 




Where I can download this FreeSurfer 6.0? 



Thanks. 



Haque 

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[Freesurfer] Brainstem segmentation

2016-05-02 Thread Haque, Muhammad E 
Dear FreeSurfer Users,

 

I would like to know if we can do brainstem segmentation as described in the
recent publication  

http://www.sciencedirect.com/science/article/pii/S1053811915001895

 

Author as well as FreeSurfer website mention that this feature is only
available in FreeSurfer 6.0 and later version

 

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

 

Where I can download this FreeSurfer 6.0?

 

Thanks.

 

Haque



smime.p7s
Description: S/MIME cryptographic signature
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