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-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
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