Re: [Freesurfer] thalamic nuclei segmentation

[Iglesias Gonzalez, Juan E.]

Dear Sara,
You can download Freesurfer 7, install it side by side with FreeSurfer 6, and 
run the thalamic module on the already reconned subjects.
Cheers,
/E


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



From:  on behalf of Sara PONTICORVO 

Reply-To: Freesurfer support list 
Date: Thursday, April 8, 2021 at 03:22
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] thalamic nuclei segmentation


External Email - Use Caution
Hi Freesurfer experts,
I processed ~150 subjects with freesurfer v6 (recon-all) and I was wondering if 
it is possible to use the script for the segmentation of the thalamic nuclei on 
these subjects.
I know this part of the processing is now integrated in the v7 of freesurfer, 
but I'm thinking if there is a way to avoid re-run all the reconstruction with 
the new version.
I looked in the wiki page, and it seems that there was a way to integrate the 
scripts in the  fs-v6, but I don't  find any downloadable package or scripts.

Thanks for your help,
Sara


--
Sara Ponticorvo, PhD
Department of Medicine Surgery and Dentistry
University of Salerno
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[Freesurfer] thalamic nuclei segmentation

[Sara PONTICORVO]

External Email - Use Caution

Hi Freesurfer experts,
I processed ~150 subjects with freesurfer v6 (recon-all) and I was
wondering if it is possible to use the script for the segmentation of the
thalamic nuclei on these subjects.
I know this part of the processing is now integrated in the v7 of
freesurfer, but I'm thinking if there is a way to avoid re-run all the
reconstruction with the new version.
I looked in the wiki page, and it seems that there was a way to integrate
the scripts in the  fs-v6, but I don't  find any downloadable package or
scripts.

Thanks for your help,
Sara


-- 
Sara Ponticorvo, PhD
Department of Medicine Surgery and Dentistry
University of Salerno
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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Thanks, Franziska.
It seems to be a problem with partial voluming. Cerebral white matter (white 
pixels) mixes with a thin layer of cerebrospinal fluid (black pixels) and the 
result is a bunch of gray pixels that look like the pulvinar. 
Partial voluming is one of the biggest problems with these Bayesian 
segmentation methods, the price you pay for the (huge!) advantage of being 
agnostic to / robust against changes in MR contrast of the input scan...
Unfortunately, there is no easy fix for this at the moment. Normally, the 
increment in volume due to the leak is not as large as it may seem because 
segmentations are weighted by their probabilities when computing volumes.
In the future, we plan to tackle this with deep learning methods that do a 
fantastic job with partial voluming. The problems with this approach are: 1. 
Robustness against contrast changes, and (mostly) 2. Training with ex vivo data 
is tricky.
Cheers,
/Eugenio

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

On 3/16/21, 03:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:

External Email - Use Caution

Dear Eugenio,

here are the zipped norm.mgz and automated segmentations for two subjects:

https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7D74Z2Par77m2PVo3Wm0nQOKU_ZQ-VZllAjpGFcJ7zfC7AlgdlnICsp__aPb0nZFYLze4Y4r4hXIerT0tQVso_xsDOOgtYVy_dklam9cgKMC-wR52zgKm5jglckTj8HXlBbyMSOoPV9vsz-z-JKtmPpLDPR8TNqyWG8oqsdSGX66xfPZQlqhlzyTmUwm1X5mSPeKecX9Fn3hcELI917WBy-1yix24jyDIneXrAWikw/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2FmzyagMpXgSmDbBo

Hope this helps!

Best regards,
Franziska


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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Eugenio,

here are the zipped norm.mgz and automated segmentations for two subjects:
https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7D74Z2Par77m2PVo3Wm0nQOKU_ZQ-VZllAjpGFcJ7zfC7AlgdlnICsp__aPb0nZFYLze4Y4r4hXIerT0tQVso_xsDOOgtYVy_dklam9cgKMC-wR52zgKm5jglckTj8HXlBbyMSOoPV9vsz-z-JKtmPpLDPR8TNqyWG8oqsdSGX66xfPZQlqhlzyTmUwm1X5mSPeKecX9Fn3hcELI917WBy-1yix24jyDIneXrAWikw/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2FmzyagMpXgSmDbBo

Hope this helps!

Best regards,
Franziska


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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Yes!

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

On 3/15/21, 08:36, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:

External Email - Use Caution

Dear Eugenio,

do you mean the "ThalamicNuclei.v12.T1.mgz" files?

Best regards,
Franziska
___

Date: Thu, 11 Mar 2021 16:29:45 +
From: "Iglesias Gonzalez, Juan E." 
Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?
To: Freesurfer support list 

Dear Franziska,
Can you please send the automated segmentations as well?
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://secure-web.cisco.com/141gcV3WY5mJIjV2uPDoq59J1j9A_zAepv_kVvEZA1jJ2mug1lkKUR5yoNaV6M0Zvtnhm3gn8yGPte_48BoO-JY_QrAoYKxlRIfkeXmYIEcdX4WSVWH2lkt3PB1C-RCyoDubggQQar_L6e5QVO_uEBOW_PyBz-3vdxwVmZwrB3FwyKaUm1BhjG90py57Ra29h_B3dzUBGPuWAXQXkdTFhTENSfFdEnYreP9UDacODv9LSjxJkwI2PSPmwCk58JnMYDvXE10_Gcr1R52k6POOK6g/http%3A%2F%2Fwww.jeiglesias.com
 


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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Eugenio,

do you mean the "ThalamicNuclei.v12.T1.mgz" files?

Best regards,
Franziska
___

Date: Thu, 11 Mar 2021 16:29:45 +
From: "Iglesias Gonzalez, Juan E." 
Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?
To: Freesurfer support list 

Dear Franziska,
Can you please send the automated segmentations as well?
Cheers,
/Eugenio

 
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/141gcV3WY5mJIjV2uPDoq59J1j9A_zAepv_kVvEZA1jJ2mug1lkKUR5yoNaV6M0Zvtnhm3gn8yGPte_48BoO-JY_QrAoYKxlRIfkeXmYIEcdX4WSVWH2lkt3PB1C-RCyoDubggQQar_L6e5QVO_uEBOW_PyBz-3vdxwVmZwrB3FwyKaUm1BhjG90py57Ra29h_B3dzUBGPuWAXQXkdTFhTENSfFdEnYreP9UDacODv9LSjxJkwI2PSPmwCk58JnMYDvXE10_Gcr1R52k6POOK6g/http%3A%2F%2Fwww.jeiglesias.com
 


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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Dear Franziska,
Can you please send the automated segmentations as well?
Cheers,
/Eugenio

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

On 3/11/21, 09:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:

External Email - Use Caution

Here are the norm.mgz files of two subjects as .zip file:

https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzIdjkIjTOvtomItfqHsdtu1RXIan9sqawThsD1AInX2PV_jNS-9gp_FPgvgzSNu5cvTJ3FuX_AJhQoY7ADXl3WDZ7EypfhlOS6dgCV2hdRIEtwFUpEFgZxu8x62DXJzDHVEYp5Edr22tcIE79zGpIu-qXANDWaexYIMUXA9XJvYhyCYYfcsyIlXrXQk9MkoF3_ONddEpAyG3iOnx4ErXzREE-nIZebs_59EE0Bp7Kgg/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2Fz53CsHgjz7rC2zj

Thanks for your help!

Best regards, Franziska


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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Here are the norm.mgz files of two subjects as .zip file:
https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzIdjkIjTOvtomItfqHsdtu1RXIan9sqawThsD1AInX2PV_jNS-9gp_FPgvgzSNu5cvTJ3FuX_AJhQoY7ADXl3WDZ7EypfhlOS6dgCV2hdRIEtwFUpEFgZxu8x62DXJzDHVEYp5Edr22tcIE79zGpIu-qXANDWaexYIMUXA9XJvYhyCYYfcsyIlXrXQk9MkoF3_ONddEpAyG3iOnx4ErXzREE-nIZebs_59EE0Bp7Kgg/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2Fz53CsHgjz7rC2zj

Thanks for your help!

Best regards, Franziska


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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Dropbox is fine.
Cheers,
/E


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



From:  on behalf of "Gronow, Franziska" 

Reply-To: Freesurfer support list 
Date: Wednesday, March 10, 2021 at 05:31
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?


External Email - Use Caution
Dear Eugenio,

thanks for your response. I wasn’t sure whether .mgz files contain patient 
information so I had to clarify that. It would be great if you could take a 
look on the affected cases. I could send you norm.mgz files of one or more 
subjects. Can I send them directly via email or do you prefer dropbox?
Thanks again!

Best regards, Franziska


--



Message: 17

Date: Tue, 23 Feb 2021 16:20:43 +

From: "Iglesias Gonzalez, Juan E." 

Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?

To: Freesurfer support list 

Message-ID: <1f81bc20-3ba0-4a5b-b507-13eed2bee...@mgh.harvard.edu>

Content-Type: text/plain; charset="utf-8"



Sure! The more slices the better __

Maybe it would be possible to share norm.mgz (which is skull stripped and thus 
deidentified) and the segmentation? Or maybe even crop norm.mgz around the 
thalami with Freeview?

Cheers,

/E





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







?On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:



External Email - Use Caution



Dear Eugenio,



thank you for your response. Unfortunately it is not possible to share the 
whole subject. Would it be helpful to send you more screenshots of all three 
views (coronal, sagittal, axial) with different mask opacities?



Kind regards,

Franziska

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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Eugenio,

thanks for your response. I wasn't sure whether .mgz files contain patient 
information so I had to clarify that. It would be great if you could take a 
look on the affected cases. I could send you norm.mgz files of one or more 
subjects. Can I send them directly via email or do you prefer dropbox?
Thanks again!

Best regards, Franziska


--



Message: 17

Date: Tue, 23 Feb 2021 16:20:43 +

From: "Iglesias Gonzalez, Juan E." 

Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?

To: Freesurfer support list 

Message-ID: <1f81bc20-3ba0-4a5b-b507-13eed2bee...@mgh.harvard.edu>

Content-Type: text/plain; charset="utf-8"



Sure! The more slices the better __

Maybe it would be possible to share norm.mgz (which is skull stripped and thus 
deidentified) and the segmentation? Or maybe even crop norm.mgz around the 
thalami with Freeview?

Cheers,

/E





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://secure-web.cisco.com/11XaMU-QoiZKnXiNuQPJicEtr4gYDxjHq1ZrbybgK3HfB2JNtRZNtkp7LR4JPl6-pJz7sJHs8M-kH8Ci1A2-q8tJMtyChK6Wqv1wSkgzw8cY2K8Au4uGqJYiUxurISKRuzojPPxghTgD1R_HeBZly0U4i-PoeTS1vwrz2qscnBKCg5bK0kZFv8yRqQgUqkhE0YMCxqMENl9178aKiHu_OjKnJ4r1DFuB193GIpdgcoVjT8aVsbV7dt5DelQ47g1joONClSugcb-lAudzsb0y5lQ/http%3A%2F%2Fwww.jeiglesias.com







?On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:



External Email - Use Caution



Dear Eugenio,



thank you for your response. Unfortunately it is not possible to share the 
whole subject. Would it be helpful to send you more screenshots of all three 
views (coronal, sagittal, axial) with different mask opacities?



Kind regards,

Franziska

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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

 > Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc
> pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q
> nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN
> FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE
> 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F
> mailman%2Flistinfo%2Ffreesurfer
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Message: 3
Date: Wed, 17 Feb 2021 17:36:49 +0900
From: ? 
Subject: [Freesurfer] VB password
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <3888b0f5-515a-4637-83f6-38e635234...@fmu.ac.jp>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi, I am attempting to run the Freesurfer Ubuntu virtual box but I need the 
?Developed? password.  Is it possible to have it?

Best

Mudathir



--

Message: 4
Date: Wed, 17 Feb 2021 08:54:00 +
From: "Gronow, Franziska" 
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus
mis-segmentation?
To: "'freesurfer@nmr.mgh.harvard.edu'"

Message-ID: 
Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

Dear Freesurfer experts,

I've been using Freesurfer 7 for only a few months. I've searched the list 
and no similar observations have been reported.
For my project I used the "Segmentation of thalamic nuclei" tool by 
Iglesias, J.E. et al.
The "recon-all" as well as the thalamic segmentation process have been run. 
For quality control an outlier script was used to identify statistical outliers.
In the course of the visual QC the PuM nucleus appeared to be mis-segmented 
in many cases - regardless of whether it was flagged as statistical outlier or 
not.
I was wondering whether others had similar experiences and whether there 
are any recommendations how to handle such cases. We thought about excluding 
this area from our analysis for all subjects. Would you recommend such a 
procedure?
I uploaded on dropbox 3 screenshots  of a typical case (with/without/low 
opacity mask) so that you get an idea of what I mean:

https://secure-web.cisco.com/13NyoIuwpnsiHWemQxkjh3X8nFYXTG9wpVXrDAWJsCjxurFVaijSCi6HJ1omS-JnHaipqYf5OTTQWIpbyRGx1_9uZDcFhQbX6Iz_gAK-PbGYNDeH6sLSwTH44gEtwTIIDN3jA24q3bDrmmkiYMtKoLeNzHyjPGySb1cHLbldpyoJgJe3zdizx9tlVc9dPMmRMk-DDBSBpmAmCPpY0ZiHiy612_W6DLESWA4wfED2Qh1qBp1OOpbisCCSiSBzrCY031mQMzsBKD7lNrvAIk8bVHA/https%3A%2F%2Fwww.dropbox.com%2Fsh%2F53fhanytrt4es6e%2FAAAqEmgl7N5YqpxDYMfxHQDAa%3Fdl%3D0

Thanks for your help!



Best,
Franziska
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Message: 5
Date: Wed, 17 Feb 2021 14:57:46 +0530
From: Koustav Chatterjee 
Subject: [Freesurfer] Queries in qdec
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Dear Forum members,

May I get your help please to resolve 2 queries below?

1. I am unable to see  .tiff files taken through 'quicksnaps.tiff' of the 
'qdec' analysed data. Even after completing the process of 'quicksnaps.tiff' 
successfully, I can see only black screen while opening the file. Please find a 
sample pic of how those files look.

[image: image.png]


2.  I am using FreeSurfer version 6 where I am *missing 'Design Matrix
Type'* inside the 'design' tab of 'qdec' command.

[image: image.png]

Thank you for your time and help.

Regards,
Koustav
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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

> 
>
>
>
> I have run this on several T1 files with similar results on each.
> FreeSurfer 6 surfaces always look smooth and refract light nicely.
> FreeSurfer 7 surfaces do not. I'm out of ideas, and the only 
> difference I can find is FreeSurfer version, so thank you to anyone 
> who can point me in the right direction to fix this issue.
>
>
>
> Mike Schmidt
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> *MailScanner has detected a possible fraud attempt from 
> "secure-web.cisco.com" claiming to be* 
> https://secure-web.cisco.com/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc
> pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q
> nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN
> FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE
> 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F
> mailman%2Flistinfo%2Ffreesurfer 
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Message: 3
Date: Wed, 17 Feb 2021 17:36:49 +0900
From: ? 
Subject: [Freesurfer] VB password
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <3888b0f5-515a-4637-83f6-38e635234...@fmu.ac.jp>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi, I am attempting to run the Freesurfer Ubuntu virtual box but I need the 
?Developed? password.  Is it possible to have it?

Best

Mudathir



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Message: 4
Date: Wed, 17 Feb 2021 08:54:00 +
From: "Gronow, Franziska" 
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus
mis-segmentation?
To: "'freesurfer@nmr.mgh.harvard.edu'"

Message-ID: 
Content-Type: text/plain; charset="us-ascii&quo

Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

PS sorry for misspelling your name! It got autocorrected into Francisca and I 
only noticed one of the wrong c:s


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



From:  on behalf of "Iglesias Gonzalez, 
Juan E." 
Reply-To: Freesurfer support list 
Date: Wednesday, February 17, 2021 at 08:54
To: Freesurfer support list 
Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?

Dear Franciska,
It’s hard to tell from a single plane, but it seems that dark voxels from the 
ventricles are mixing with bright voxels from the corpus callosum, into gray 
voxels looking like the pulvinar and medical nuclei.
Would you be able to share the whole subject so I can take a closer look?
Cheers,
/E


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



From:  on behalf of "Gronow, Franziska" 

Reply-To: Freesurfer support list 
Date: Wednesday, February 17, 2021 at 03:54
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?


External Email - Use Caution
Dear Freesurfer experts,

I’ve been using Freesurfer 7 for only a few months. I've searched the list and 
no similar observations have been reported.
For my project I used the „Segmentation of thalamic nuclei“ tool by Iglesias, 
J.E. et al.
The „recon-all“ as well as the thalamic segmentation process have been run. For 
quality control an outlier script was used to identify statistical outliers.
In the course of the visual QC the PuM nucleus appeared to be mis-segmented in 
many cases – regardless of whether it was flagged as statistical outlier or not.
I was wondering whether others had similar experiences and whether there are 
any recommendations how to handle such cases. We thought about excluding this 
area from our analysis for all subjects. Would you recommend such a procedure?
I uploaded on dropbox 3 screenshots  of a typical case (with/without/low 
opacity mask) so that you get an idea of what I mean:
https://www.dropbox.com/sh/53fhanytrt4es6e/AAAqEmgl7N5YqpxDYMfxHQDAa?dl=0

Thanks for your help!



Best,
Franziska
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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Dear Franciska,
It’s hard to tell from a single plane, but it seems that dark voxels from the 
ventricles are mixing with bright voxels from the corpus callosum, into gray 
voxels looking like the pulvinar and medical nuclei.
Would you be able to share the whole subject so I can take a closer look?
Cheers,
/E


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



From:  on behalf of "Gronow, Franziska" 

Reply-To: Freesurfer support list 
Date: Wednesday, February 17, 2021 at 03:54
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?


External Email - Use Caution
Dear Freesurfer experts,

I’ve been using Freesurfer 7 for only a few months. I've searched the list and 
no similar observations have been reported.
For my project I used the „Segmentation of thalamic nuclei“ tool by Iglesias, 
J.E. et al.
The „recon-all“ as well as the thalamic segmentation process have been run. For 
quality control an outlier script was used to identify statistical outliers.
In the course of the visual QC the PuM nucleus appeared to be mis-segmented in 
many cases – regardless of whether it was flagged as statistical outlier or not.
I was wondering whether others had similar experiences and whether there are 
any recommendations how to handle such cases. We thought about excluding this 
area from our analysis for all subjects. Would you recommend such a procedure?
I uploaded on dropbox 3 screenshots  of a typical case (with/without/low 
opacity mask) so that you get an idea of what I mean:
https://www.dropbox.com/sh/53fhanytrt4es6e/AAAqEmgl7N5YqpxDYMfxHQDAa?dl=0

Thanks for your help!



Best,
Franziska
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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Freesurfer experts,

I've been using Freesurfer 7 for only a few months. I've searched the list and 
no similar observations have been reported.
For my project I used the "Segmentation of thalamic nuclei" tool by Iglesias, 
J.E. et al.
The "recon-all" as well as the thalamic segmentation process have been run. For 
quality control an outlier script was used to identify statistical outliers.
In the course of the visual QC the PuM nucleus appeared to be mis-segmented in 
many cases - regardless of whether it was flagged as statistical outlier or not.
I was wondering whether others had similar experiences and whether there are 
any recommendations how to handle such cases. We thought about excluding this 
area from our analysis for all subjects. Would you recommend such a procedure?
I uploaded on dropbox 3 screenshots  of a typical case (with/without/low 
opacity mask) so that you get an idea of what I mean:
https://secure-web.cisco.com/13NyoIuwpnsiHWemQxkjh3X8nFYXTG9wpVXrDAWJsCjxurFVaijSCi6HJ1omS-JnHaipqYf5OTTQWIpbyRGx1_9uZDcFhQbX6Iz_gAK-PbGYNDeH6sLSwTH44gEtwTIIDN3jA24q3bDrmmkiYMtKoLeNzHyjPGySb1cHLbldpyoJgJe3zdizx9tlVc9dPMmRMk-DDBSBpmAmCPpY0ZiHiy612_W6DLESWA4wfED2Qh1qBp1OOpbisCCSiSBzrCY031mQMzsBKD7lNrvAIk8bVHA/https%3A%2F%2Fwww.dropbox.com%2Fsh%2F53fhanytrt4es6e%2FAAAqEmgl7N5YqpxDYMfxHQDAa%3Fdl%3D0

Thanks for your help!



Best,
Franziska
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Re: [Freesurfer] Thalamic nuclei segmentation

[Douglas N. Greve]

It will ignore the projmap option, so you can just leave it as X (it can 
be any string, but there does have to be something there). For the reg, 
use regheader



On 6/4/2020 6:00 AM, Quentin Devignes wrote:


External Email - Use Caution

Dear Doctor Greve,

Thank you for your reply. I am trying to do what you advised me.

For now, I have segmented thalamic nuclei in the left hemisphere, 
checked and corrected this segmentation and used MRI_binarize as 
advised. However, I don’t know what to write for the « projmap » 
option of vol2surf… Could you please help me?


My command line is: vol2surf --vol2surf ***the thalamic 
segmentation.mgz*** ***the surface obtained from MRI_binarize*** 1 
(for projtype option) -2 (for projdist option) X (nothing for projmap 
option) ‘lta’ (for reg option) ’novsm’ (for vsm option) 0 (for interp 
option) ***My directory*** (for output option).


Wish you a nice day,
Best regards,

Quentin DEVIGNES
PhD candidate in neurosciences
Neuropsychologist
UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE

Le 1 juin 2020 à 16:40, Douglas N. Greve > a écrit :


You can create a surface using mri_binarize listing all the thalamic 
nuclei with --match and specifying a surface output (you may wan to 
smooth it a little bit to remove the pixelization). You can then use 
mri_vol2surf (using the vol2surf in the link below with the 
--vol2surf option  and using the thalamic segmentation itself as the 
input volume, abs for the projtype and maybe -2 mm for the projdist 
and interp 0 for nearest). You can then use mris_seg2annot to create 
an annotation that you can visualize on the surface.



https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf

On 6/1/2020 5:33 AM, Quentin Devignes wrote:


External Email - Use Caution

Dear Doctor Iglesias,

Thanks for your previous reply. As agreed, I post my question on the 
Freesurfer list.


We are doing shape analyses on thalamus in order to determine 
whether distinct cognitive profiles in Parkinson’s disease have 
different deformation fiels of the thalamic surface. We used 
SPHARM-PDM tool (shape analysis module in Slicer4) to obtain 
deformation fields and p-values map (cf. attached file; vectors 
represent the magnitude of deformation between two groups).We are 
not developing a new method, we used an existing one (SPHARM-PDM). 
However, to be more accurate, we would like to delineate thalamic 
nuclei on the surface of our meshes (because the nuclei have 
different functional role). Existing atlases (such as yours) are 
usable on volumes but not on surfaces. Do you have any idea how we 
could project your atlas onto a surface? We did not find any method 
in the scientific literature.


Hope you could help us,
Best regards,

Quentin DEVIGNES
PhD candidate in neurosciences
Neuropsychologist
UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE




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Re: [Freesurfer] Thalamic nuclei segmentation

[Quentin Devignes]

External Email - Use Caution

Dear Doctor Greve, 

Thank you for your reply. I am trying to do what you advised me. 

For now, I have segmented thalamic nuclei in the left hemisphere, checked and 
corrected this segmentation and used MRI_binarize as advised. However, I don’t 
know what to write for the « projmap » option of vol2surf… Could you please 
help me?

My command line is: vol2surf --vol2surf ***the thalamic segmentation.mgz*** 
***the surface obtained from MRI_binarize*** 1 (for projtype option) -2 (for 
projdist option) X (nothing for projmap option) ‘lta’ (for reg option) ’novsm’ 
(for vsm option) 0 (for interp option) ***My directory*** (for output option). 

Wish you a nice day, 
Best regards, 

Quentin DEVIGNES
PhD candidate in neurosciences
Neuropsychologist
UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE

> Le 1 juin 2020 à 16:40, Douglas N. Greve  a écrit :
> 
> You can create a surface using mri_binarize listing all the thalamic nuclei 
> with --match and specifying a surface output (you may wan to smooth it a 
> little bit to remove the pixelization). You can then use mri_vol2surf (using 
> the vol2surf in the link below with the --vol2surf option  and using the 
> thalamic segmentation itself as the input volume, abs for the projtype and 
> maybe -2 mm for the projdist and interp 0 for nearest). You can then use 
> mris_seg2annot to create an annotation that you can visualize on the surface.
> 
> 
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf 
> 
> 
> On 6/1/2020 5:33 AM, Quentin Devignes wrote:
>> External Email - Use Caution
>> 
>> Dear Doctor Iglesias, 
>> 
>> Thanks for your previous reply. As agreed, I post my question on the 
>> Freesurfer list. 
>> 
>> We are doing shape analyses on thalamus in order to determine whether 
>> distinct cognitive profiles in Parkinson’s disease have different 
>> deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape 
>> analysis module in Slicer4) to obtain deformation fields and p-values map 
>> (cf. attached file; vectors represent the magnitude of deformation between 
>> two groups).We are not developing a new method, we used an existing one 
>> (SPHARM-PDM). However, to be more accurate, we would like to delineate 
>> thalamic nuclei on the surface of our meshes (because the nuclei have 
>> different functional role). Existing atlases (such as yours) are usable on 
>> volumes but not on surfaces. Do you have any idea how we could project your 
>> atlas onto a surface? We did not find any method in the scientific 
>> literature. 
>> 
>> Hope you could help us, 
>> Best regards, 
>> 
>> Quentin DEVIGNES
>> PhD candidate in neurosciences
>> Neuropsychologist
>> UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
>> 
>> 
>> 
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
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Re: [Freesurfer] Thalamic nuclei segmentation

[Iglesias Gonzalez, Juan E.]

Please try:
segmentThalamicNuclei.sh   4001   
/Applications/freesurfer_dev/freesurfer/subjects/  
/Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii
T2_THALAMUSt2
Cheers,
/Eugenio

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


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Sunday, 8 December 2019 at 15:00
To: Freesurfer support list 
Subject: [Freesurfer] Thalamic nuclei segmentation

segmentThalamicNuclei.sh 4001 
/Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS 
BBREGISTER_MODE t2
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[Freesurfer] Thalamic nuclei segmentation

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Dear Freesurfer devs,

I tried to run the thalamic nuclei segmentation (T1 and T2 as input) using
the freesurfer dev version and the terminal gave to me the following error


rmnlab1:~ neucoga$ segmentThalamicNuclei.sh 4001
/Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii
THALAMUS BBREGISTER_MODE t2

Setting ITK threads to 1

#

#@# Thalamic Nuclei processing domingo,  8 de diciembre de 2019, 20:55:24
CET

--

Setting up environment variables

---

DYLD_LIBRARY_PATH is
.:/Applications/freesurfer_dev/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib

Error using SegmentThalamicNuclei (line 138)

Additional volume does not exist



255

Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21
22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64


Thalamic nuclei exited with ERRORS at domingo,  8 de diciembre de 2019,
20:55:31 CET


For more details, see the log file
/Applications/freesurfer_dev/freesurfer/subjects/4001/scripts/thalamic-nuclei-BBREGISTER_MODE.log




Is the command right? I think that I have followed correctly the
instructions of the website.


Best regards,
-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Thalamic nuclei segmentation

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Zheng,
Did the segmentation run to completion?
Can you please send us the output?
Cheers
Eugenio

Sent from mobile, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 郑凤莲 

Sent: Wednesday, March 27, 2019 3:09:21 AM
To: Freesurfer support list
Subject: [Freesurfer] Thalamic nuclei segmentation


External Email - Use Caution

Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version. 
However, when I input "freeview -v nu.mgz -v 
ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview, 
just nu.mgz. What's the matter? Please help me. I am looking forward to your 
reply. Thanks very much.
Sincerely,
Zheng




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[Freesurfer] Thalamic nuclei segmentation

[郑凤莲]

External Email - Use Caution

Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version. 
However, when I input "freeview -v nu.mgz -v 
ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview, 
just nu.mgz. What's the matter? Please help me. I am looking forward to your 
reply. Thanks very much.
Sincerely,
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Re: [Freesurfer] Thalamic nuclei segmentation

[Greve, Douglas N.,Ph.D.]

http://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei

On 2/14/19 2:21 PM, Antti Cajanus wrote:
>  External Email - Use Caution
>
> Hi!
>
> Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer 
> development version and I had it working fine. However, I can’t find the web 
> page anymore with the instructions how to use the tool. Is the tool still in 
> use and if so, where can I find the instructions? Also, does free surfer have 
> a similar segmentation tool for cerebellar subsegments? Thank you in advance!
>
> -Antti
>
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[Freesurfer] Thalamic nuclei segmentation

[Antti Cajanus]

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Hi!

Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer 
development version and I had it working fine. However, I can’t find the web 
page anymore with the instructions how to use the tool. Is the tool still in 
use and if so, where can I find the instructions? Also, does free surfer have a 
similar segmentation tool for cerebellar subsegments? Thank you in advance!

-Antti

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Re: [Freesurfer] Thalamic Nuclei segmentation results

[Iglesias Gonzalez, Eugenio]

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Hi Vasudev,

What lookup table are you using to visualize the results? Are you using 
FreeView from the development version, and visualizing the segmentation with 
the default lookup table?

Cheers,

/Eugenio


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dev vasu 

Sent: Tuesday, October 9, 2018 10:06:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Thalamic Nuclei segmentation results


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Dear all,

I have used Freesurfer pipeline for Thalamic  Nuclei segmentation, the results 
of segmentation appear to be very poor, i am annexing the results , please 
kindly review if there is any thing wrong with the segmentation results.


Thanks
Vasudev
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[Freesurfer] Thalamic Nuclei segmentation results

[Dev vasu]

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Dear all,

I have used Freesurfer pipeline for Thalamic  Nuclei segmentation, the
results of segmentation appear to be very poor, i am annexing the results ,
please kindly review if there is any thing wrong with the segmentation
results.


Thanks
Vasudev
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[Freesurfer] Thalamic Nuclei segmentation

[Miguel Ángel Rivas Fernández]

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Hi Freesurfer devs,


Just a simple question, it´s possible make the thalamic nuclei segmentation
using as input a simple T2 image as additional scan or by contrary, is
always required use as input a more specific scan such as the FGATIR or a
DBS scan.



Best,

-- 
*Miguel Ángel Rivas Fernández*
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