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... . 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... https://secure-web.cisco.com/12zaO7jd5zPchZlNamn2OOwsicMw7Cg6FNxaL13gnPuKZwQ...
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Katharina von Kriegstein katharina.von_kriegstein@tu-dresden.de Date: Monday, February 26, 2024 at 5:16 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Chelsea Jarrett chelsea.jarrett@tu-dresden.de, Hannes Ruge hannes.ruge@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... . 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... https://secure-web.cisco.com/12zaO7jd5zPchZlNamn2OOwsicMw7Cg6FNxaL13gnPuKZwQ...
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_QjeJlPSOKUOHiSa...
Best regards,
Katharina
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Iglesias Gonzalez, Juan E. Gesendet: Montag, 26. Februar 2024 16:26 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Jarrett, Chelsea chelsea.jarrett@tu-dresden.de; Ruge, Hannes hannes.ruge@tu-dresden.de 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-wBNZ1ih6...
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Katharina von Kriegstein <katharina.von_kriegstein@tu-dresden.de mailto:katharina.von_kriegstein@tu-dresden.de > Date: Monday, February 26, 2024 at 5:16 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Cc: Chelsea Jarrett <chelsea.jarrett@tu-dresden.de mailto:chelsea.jarrett@tu-dresden.de >, Hannes Ruge <hannes.ruge@tu-dresden.de mailto:hannes.ruge@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 dX9M2GouB7NYbZHVyChWUizy2CDyBxGW2ytYWpVmHsL_Yl48XqOPd7RRrD5_VubAYPTw57jG_Id1 ixEfKRa3JVLCuG9ldaITVPZW72IIQxoc2VCuLI9F8TZuCgOWi0fBwgYTAW6J7oyYjlnVznnGeUvu 4fTyQfrtqcMiZWawpftG7sQ4Ql9z2Mjx2RK9ssj48uOw0o/https%3A%2F%2Fbsky.app%2Fprof ile%2Fkvonkriegstein.bsky.social
External Email - Use Caution
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Katharina von Kriegstein