subject:"\[Freesurfer\] Too large volumes thalamus segmentation in version 7.2"

Re: [Freesurfer] Too large volumes thalamus segmentation in version 7.2

2024-02-27 Thread Katharina von Kriegstein

Dear Eugenio,

 

Many thanks for your quick reply and clarification! We have uploaded example
participants here:

 

 
<https://secure-web.cisco.com/1tCYmH4ys2Ehvq0B3eB5Zbf-42HpiQJ_QjeJlPSOKUOHiSaoKM7G1CJmkDrBGcWITd4sO5bevhk53oklpAo_K39tf4TOqpWbzmo4yklOyAubIj-XKBL-8c4S47dbZzsvTAhvA6mCTmUXV_kO-bgz-IOL2z5aJH4L9KI3r9hi5LoBGx1JXVgZVtZ3gaH5WuRwZiLR95XM3ZP6B7g2tv-oUpEhgyeTsAMkzpvASFrfFXo_UwV175QXubw5UFgaiDMvbMS9ehXcjd9AC4GcyC-DoychE_cEthe0wJCR9jKpRggDSilii9EJr5xvqW_VrAHej/https%3A%2F%2Fdatashare.tu-dresden.de%2Fs%2FAtiYcQqSK7jCr8Q>
https://secure-web.cisco.com/1tCYmH4ys2Ehvq0B3eB5Zbf-42HpiQJ_QjeJlPSOKUOHiSaoKM7G1CJmkDrBGcWITd4sO5bevhk53oklpAo_K39tf4TOqpWbzmo4yklOyAubIj-XKBL-8c4S47dbZzsvTAhvA6mCTmUXV_kO-bgz-IOL2z5aJH4L9KI3r9hi5LoBGx1JXVgZVtZ3gaH5WuRwZiLR95XM3ZP6B7g2tv-oUpEhgyeTsAMkzpvASFrfFXo_UwV175QXubw5UFgaiDMvbMS9ehXcjd9AC4GcyC-DoychE_cEthe0wJCR9jKpRggDSilii9EJr5xvqW_VrAHej/https%3A%2F%2Fdatashare.tu-dresden.de%2Fs%2FAtiYcQqSK7jCr8Q

 

Best regards,

Katharina

 

 

 

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Iglesias
Gonzalez, Juan E.
Gesendet: Montag, 26. Februar 2024 16:26
An: Freesurfer support list 
Cc: Jarrett, Chelsea ; Ruge, Hannes

Betreff: Re: [Freesurfer] Too large volumes thalamus segmentation in version
7.2

 

Dear Katharina,

First of all, and to avoid any confusion, the bug only affected the script
to gather the volumes from different subjects ("quantifyThalamicNuclei.sh"),
and not the segmentations themselves.

Would you mind sharing some images, showing how/where the LGN is
oversegmented, please? It would be very helpful to better understand the
problem.

Kind regards,

/Eugenio

 

--

Juan Eugenio Iglesias

http://secure-web.cisco.com/1QoIHWx0-hhjdJ0DHeheLrwQhSDhTxo2XFs4j5D-wBNZ1ih6sPPQa2t13EECj5Df99U7LY8RGoIyAjBi2MQ6IZNBKFqsEhCaCedMvm2IrHmMbqabcwaZSor4gBsQob8wCMYvn9C08bR0VCspvYjMVmnfzcHedoy8pxV_u8NaU2hAXrVAeJfeNJsalCsA-zW0CrpGybs4sh3Bq_qm7u6iiZ8WuDy9EsvTFAgexWCNkM0RRt09ySDyAVsp3BRPW6013DbwJT7tWomQi_dquOdGaCB5X6jiByiu-OSW67rhdMDsJ9heMidoHybr-QiQcCYon/http%3A%2F%2Fwww.jeiglesias.com

 

From: freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Katharina von
Kriegstein mailto:katharina.von_kriegst...@tu-dresden.de> >
Date: Monday, February 26, 2024 at 5:16 AM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu> >
Cc: Chelsea Jarrett mailto:chelsea.jarr...@tu-dresden.de> >, Hannes Ruge
mailto:hannes.r...@tu-dresden.de> >
Subject: [Freesurfer] Too large volumes thalamus segmentation in version 7.2

Dear List,

We are using the thalamic segmentation and have encountered too large nuclei
volumes. We are aware of the bug in previous Freesurfer versions reported
here 
https://secure-web.cisco.com/1IbBjsoyLKSxbo51anCmnlGJ7AZlAHQC-iMHoutsQKt5emo
sDTMTW0h4Zr4x8Fc3T9saf02_wRcDR4wCu6Bbm5CK3KosJDQPCWk4MW2zsevWOrjnSh5jM2PW-7j
yJglBbcd_IBcCbhj_w5aPS8oA8bdObZ2aQtO0bkdTaFt-ZXIN_6DMcK3rdono_RSBISep330s0lC
-NWLL2L995DdOML88nS0YAsEYEHjhvIbvRvggLG_elezRlsrqWsMD5NxHP-plyRmABs74rTKJp7V
aC_-aW9rIG1-vzaz7ad-hqGB27LbybsrMc4ojdXtNr86G-/https%3A%2F%2Ffreesurfer.net%
2Ffswiki%2FThalamicNuclei . In version 7.2 this bug is
fixed.

Does someone else have similar difficulties with too large volumes? For
example, our LGN is 259 mm3 (left) and 304 mm3 (right), while in the
original paper for the thalamus segmentation (Iglesias et al. 2018), it is
124 mm3, which is close to the size reported by histological studies. 

Thanks for reading!
Katharina

_ _ 

Katharina von Kriegstein 

Professor of Cognitive and Clinical Neuroscience
Vice-Dean Faculty of Psychology

TUD Dresden University of Technology 
Chemnitzer Str. 48b, 01187 Dresden

Phone +49 (0) 351-463-43145 

https://secure-web.cisco.com/1gJ3pcdCtydEP4JcYC_B04s_xcYKuSS0r7VoHh7Z0azmyON
_SOw9d7jFsHvxZnQbDLToHs7ih4CjHKdZD-Epj7z6RUkQhkzm4TfzeashKffMLIkhK_AcL7TU2A6
XgvGjSsmu8ILnQVdymDWmtg7TbbqCwn-5dFhXcUFDlZ29ROUAY1RbhbCtjwV03w8FQLZFq796CYF
YeLFq3Hbto4al8LO0zLFqwNUgEMw-INgT02g6jSxVoWU2qEWsaprGKAv9XJb5SdMappHS8eZqllb
x_zohEs4ypmVRtqeOpgQpgfRLWEPWq8si77YV_au9xVW0v/https%3A%2F%2Ftu-dresden.de%2
Fmn%2Fpsychologie%2Fifap%2Fkknw
https://secure-web.cisco.com/12zaO7jd5zPchZlNamn2OOwsicMw7Cg6FNxaL13gnPuKZwQ
30XI9-8Ip0KsBo7r_BKfON8WP-YzW49Aa-LqPoPo-A8zF0q9pYN4b4MrGl_jP9me9h5lgp4-c0X6
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ixEfKRa3JVLCuG9ldaITVPZW72IIQxoc2VCuLI9F8TZuCgOWi0fBwgYTAW6J7oyYjlnVznnGeUvu
4fTyQfrtqcMiZWawpftG7sQ4Ql9z2Mjx2RK9ssj48uOw0o/https%3A%2F%2Fbsky.app%2Fprof
ile%2Fkvonkriegstein.bsky.social



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Re: [Freesurfer] Too large volumes thalamus segmentation in version 7.2

2024-02-26 Thread Iglesias Gonzalez, Juan E.

Dear Katharina,
First of all, and to avoid any confusion, the bug only affected the script to 
gather the volumes from different subjects (“quantifyThalamicNuclei.sh”), and 
not the segmentations themselves.
Would you mind sharing some images, showing how/where the LGN is oversegmented, 
please? It would be very helpful to better understand the problem.
Kind regards,
/Eugenio

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katharina von Kriegstein 

Date: Monday, February 26, 2024 at 5:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Chelsea Jarrett , Hannes Ruge 

Subject: [Freesurfer] Too large volumes thalamus segmentation in version 7.2
Dear List,

We are using the thalamic segmentation and have encountered too large nuclei
volumes. We are aware of the bug in previous Freesurfer versions reported
here
https://secure-web.cisco.com/1IbBjsoyLKSxbo51anCmnlGJ7AZlAHQC-iMHoutsQKt5emosDTMTW0h4Zr4x8Fc3T9saf02_wRcDR4wCu6Bbm5CK3KosJDQPCWk4MW2zsevWOrjnSh5jM2PW-7jyJglBbcd_IBcCbhj_w5aPS8oA8bdObZ2aQtO0bkdTaFt-ZXIN_6DMcK3rdono_RSBISep330s0lC-NWLL2L995DdOML88nS0YAsEYEHjhvIbvRvggLG_elezRlsrqWsMD5NxHP-plyRmABs74rTKJp7VaC_-aW9rIG1-vzaz7ad-hqGB27LbybsrMc4ojdXtNr86G-/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei
 . In version 7.2 this bug is
fixed.

Does someone else have similar difficulties with too large volumes? For
example, our LGN is 259 mm3 (left) and 304 mm3 (right), while in the
original paper for the thalamus segmentation (Iglesias et al. 2018), it is
124 mm3, which is close to the size reported by histological studies.

Thanks for reading!
Katharina

_ _

Katharina von Kriegstein

Professor of Cognitive and Clinical Neuroscience
Vice-Dean Faculty of Psychology

TUD Dresden University of Technology
Chemnitzer Str. 48b, 01187 Dresden

Phone +49 (0) 351-463-43145

https://secure-web.cisco.com/1gJ3pcdCtydEP4JcYC_B04s_xcYKuSS0r7VoHh7Z0azmyON_SOw9d7jFsHvxZnQbDLToHs7ih4CjHKdZD-Epj7z6RUkQhkzm4TfzeashKffMLIkhK_AcL7TU2A6XgvGjSsmu8ILnQVdymDWmtg7TbbqCwn-5dFhXcUFDlZ29ROUAY1RbhbCtjwV03w8FQLZFq796CYFYeLFq3Hbto4al8LO0zLFqwNUgEMw-INgT02g6jSxVoWU2qEWsaprGKAv9XJb5SdMappHS8eZqllbx_zohEs4ypmVRtqeOpgQpgfRLWEPWq8si77YV_au9xVW0v/https%3A%2F%2Ftu-dresden.de%2Fmn%2Fpsychologie%2Fifap%2Fkknw
https://secure-web.cisco.com/12zaO7jd5zPchZlNamn2OOwsicMw7Cg6FNxaL13gnPuKZwQ30XI9-8Ip0KsBo7r_BKfON8WP-YzW49Aa-LqPoPo-A8zF0q9pYN4b4MrGl_jP9me9h5lgp4-c0X6dX9M2GouB7NYbZHVyChWUizy2CDyBxGW2ytYWpVmHsL_Yl48XqOPd7RRrD5_VubAYPTw57jG_Id1ixEfKRa3JVLCuG9ldaITVPZW72IIQxoc2VCuLI9F8TZuCgOWi0fBwgYTAW6J7oyYjlnVznnGeUvu4fTyQfrtqcMiZWawpftG7sQ4Ql9z2Mjx2RK9ssj48uOw0o/https%3A%2F%2Fbsky.app%2Fprofile%2Fkvonkriegstein.bsky.social
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[Freesurfer] Too large volumes thalamus segmentation in version 7.2

2024-02-26 Thread Katharina von Kriegstein

Dear List,

We are using the thalamic segmentation and have encountered too large nuclei
volumes. We are aware of the bug in previous Freesurfer versions reported
here 
https://secure-web.cisco.com/1IbBjsoyLKSxbo51anCmnlGJ7AZlAHQC-iMHoutsQKt5emosDTMTW0h4Zr4x8Fc3T9saf02_wRcDR4wCu6Bbm5CK3KosJDQPCWk4MW2zsevWOrjnSh5jM2PW-7jyJglBbcd_IBcCbhj_w5aPS8oA8bdObZ2aQtO0bkdTaFt-ZXIN_6DMcK3rdono_RSBISep330s0lC-NWLL2L995DdOML88nS0YAsEYEHjhvIbvRvggLG_elezRlsrqWsMD5NxHP-plyRmABs74rTKJp7VaC_-aW9rIG1-vzaz7ad-hqGB27LbybsrMc4ojdXtNr86G-/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei
 . In version 7.2 this bug is
fixed.

Does someone else have similar difficulties with too large volumes? For
example, our LGN is 259 mm3 (left) and 304 mm3 (right), while in the
original paper for the thalamus segmentation (Iglesias et al. 2018), it is
124 mm3, which is close to the size reported by histological studies. 

Thanks for reading!
Katharina

_ _ 

Katharina von Kriegstein 

Professor of Cognitive and Clinical Neuroscience
Vice-Dean Faculty of Psychology

TUD Dresden University of Technology 
Chemnitzer Str. 48b, 01187 Dresden

Phone +49 (0) 351-463-43145 

https://secure-web.cisco.com/1gJ3pcdCtydEP4JcYC_B04s_xcYKuSS0r7VoHh7Z0azmyON_SOw9d7jFsHvxZnQbDLToHs7ih4CjHKdZD-Epj7z6RUkQhkzm4TfzeashKffMLIkhK_AcL7TU2A6XgvGjSsmu8ILnQVdymDWmtg7TbbqCwn-5dFhXcUFDlZ29ROUAY1RbhbCtjwV03w8FQLZFq796CYFYeLFq3Hbto4al8LO0zLFqwNUgEMw-INgT02g6jSxVoWU2qEWsaprGKAv9XJb5SdMappHS8eZqllbx_zohEs4ypmVRtqeOpgQpgfRLWEPWq8si77YV_au9xVW0v/https%3A%2F%2Ftu-dresden.de%2Fmn%2Fpsychologie%2Fifap%2Fkknw
https://secure-web.cisco.com/12zaO7jd5zPchZlNamn2OOwsicMw7Cg6FNxaL13gnPuKZwQ30XI9-8Ip0KsBo7r_BKfON8WP-YzW49Aa-LqPoPo-A8zF0q9pYN4b4MrGl_jP9me9h5lgp4-c0X6dX9M2GouB7NYbZHVyChWUizy2CDyBxGW2ytYWpVmHsL_Yl48XqOPd7RRrD5_VubAYPTw57jG_Id1ixEfKRa3JVLCuG9ldaITVPZW72IIQxoc2VCuLI9F8TZuCgOWi0fBwgYTAW6J7oyYjlnVznnGeUvu4fTyQfrtqcMiZWawpftG7sQ4Ql9z2Mjx2RK9ssj48uOw0o/https%3A%2F%2Fbsky.app%2Fprofile%2Fkvonkriegstein.bsky.social



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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Too large volumes thalamus segmentation in version 7.2

Re: [Freesurfer] Too large volumes thalamus segmentation in version 7.2

[Freesurfer] Too large volumes thalamus segmentation in version 7.2

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