[Freesurfer] Postdoc position in Medical Image Computing

2024-01-15 Thread Diers, Kersten /DZNE 
External Email - Use Caution

The German Center for Neurodegenerative Diseases (DZNE) is a world-
leading internationally oriented research center, committed to
discovering new approaches to prevent and treat neurodegenerative
diseases. To this end, researchers at ten DZNE sites across Germany
pursue a translational and interdisciplinary strategy comprising five
interconnected areas: fundamental research, clinical research, health
care research, population health science, and systems medicine. 

We are looking for a postdoctoral researcher in Medical Image Computing
to join the research group of Prof. Martin Reuter (DeepMI Lab) at the
German Center for Neurodegenerative Diseases (DZNE) in Bonn, Germany.

The research focus of the DeepMI lab 
(https://secure-web.cisco.com/1MThzC1peUCNro2lFQjLKa18yzb6Hpg-Si0c_KIJ2lS10sT_UulZFjUkx7wh_hwbRctm1lFHHpx8ImjeAMGm-JQez6gtCAJ0m80cwJOPjraHQJFitfuT5NZvdZJpRPXlp7zq-LmviV7DRJye7XGtMvc0vM0vjH1zwIDBMIx0ivFBr8cGpKCH3Z-1fCe3cOp12mfp7SOsNKJZOnCCu5yzBfHXtIShOfCCvA9ELlk_rbTPnikISXhN5xITmvGQf6G9i_xD1iSf_Kf2uXH7Qd2B4NNbx0AfVxYeHLuKj-e3dVBttuN0ropRaZbdrpBcJmKTxm_GflG1l9po1HjSU2A3i9Q/https%3A%2F%2Fdeep-mi.org)
 is on the
development of novel AI methods for the automated analysis of medical
images, and on providing accessible and useful open-source software
tools for the medical imaging community. In addition to medical image
computing and computational neuroimaging, our research interests
include computational geometry and topology, computer vision, and
statistical modeling. In close collaboration with clinical and
industrial partners, we develop the next-generation computational
techniques and open-source software tools 
(https://secure-web.cisco.com/1x5I_D6HZMoyenb6ROM07HEyfo1-6i4RLvoIUTkcQNenQoqyLTs3KQsep59yWxzJzy9lr7fBEZ0ObOLZmMOKeyE-vSeXO0-bNCmmYG4_TO5Wu0uwHaxGV4R7S7h-MYmY-Y2kSszQbEQxo_Z9qjkfjCHt6nEbLby755ef7RSYhv_aQVpeuLysCyFuhnHoeTG_9uz2qbrI8Gbv9J7grB0RZtN8QcoBWi5oCVVIDhw-9EZFNjFrFCoz-ogWI8VkHnmSbLRzG4XNh5G3oljX1aWFQ2Lb9mDr0p0QbwZjupNukpY7jDnwWU8l8BuQHqF94voijv6QZAEwVQWDkoyklf6WU9Q/https%3A%2F%2Fgithub.com%2FDeep-MI)
for the analysis of large biomedical image datasets – such as
FastSurfer 
(https://secure-web.cisco.com/18DvIli8JaO37YJWJOJ3qq1WWQmz42f76xdZHIj0fW_8UF1ZhHM3FCQHvGsFzibZhx60zsN95b_ICRMtHDtGuVjQ8pkwV74_pkfsSJIVMJf8m5AgcF8iJ2YRtva41ck9gnusHtBxJYJKO3zteH0Qx769PgsKA-HyJ8c0xLUglszc5E-o9k7cZFK4rcZPp_V70fv2fj-KzaBS8n3Om5jeb01OquqjMuYo9UsoPJ7oF-35v1ZcOiB90G5IPBWHT4wwu4LPCOtIUn7mwkZ_jmqrVXIpJQJw8lO1wipEjHRWP3xrA0KcrgLFF65Y50mjKrfQaou87XzmU_zTctTjIah-EdQ/https%3A%2F%2Fdeep-mi.org%2Fresearch%2Ffastsurfer),
 a fast and
extensively validated deep-learning pipeline for the automated
processing of structural human brain MRIs that is used by neuroimaging
researchers worldwide. Our network within DZNE and the University
Clinic Bonn, as well as our close ties to the Harvard Medical School
promote our interdisciplinary research and foster deep international
collaborations.

Creative, highly motivated applicants who are willing to develop novel
deep learning image analysis methods and enjoy teamwork and working
independently in a stimulating scientific environment are encouraged to
apply.

Requirements:

- PhD degree in Computer Science or a related discipline; candidates
who are expected to complete their PhD degree soon will also be
considered.
- Solid background in Machine Learning / Deep Learning and strong
computational skills.
- Programming experience (Python) and familiarity with Machine Learning
Frameworks (e.g., PyTorch, Tensorflow).
- Experience in magnetic resonance imaging, medical image analysis,
and/or computer vision is an advantage.
 
To apply, please upload your application including a cover letter
stating your motivation and research interests, CV, relevant
transcripts and up to two references via the following link:
https://secure-web.cisco.com/1T2gF-0AOy7jeB4jbnIw5lbkhOm3NWFidBlXUXn7AZpaMDH_fS7CzlvRQxuuZ05YzHRPuCAtPV8Ydm-l85RExgTK1OmWHOtFs2pNeE-SswN0KM5oAdsNc9O9NUKpbo-iKb6kBNp5Wvj0aPCIobzIUD0wbK_oR0URE3aIDbFkGIiacAA0dAAyxuN51vorLjMT23s8unD7Vj6-LieIZrrGwhR4fE5vUQ8EFHjCpb7LdDp8SZvhot5fSp0a_PLyUIb4eejNY4jJwwA81sxZJVFVv7jX2zRjt_x-ckujKkMtRPXKFgcZc2YJSGo7bHMsZhHgAoBbl4_PD72k77FPQqYaWEA/https%3A%2F%2Fjobs.dzne.de%2Fen%2Fjobs%2F101264

The application deadline is January 30, 2024. Review of applications
will begin immediately and continue until the position is filled.

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[Freesurfer] Midline white/pial surface

2024-01-15 Thread Sunniva Fenn-Moltu 
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Hi,

i'm running recon-all and have encountered an issue with the surface boundaries 
on several subjects. What I'm experiencing is that the midline surface is 
included in the white surface in one hemisphere, and in the pial surface on the 
other hemisphere. This results in the midline boundary of the thalamus and 
ventral DC being white surface in one hemisphere, and pial surface in the 
other. Do you have any idea why this is happening?

I am running freesurfer on NoMachine (freesurfer/7.4.1).

Best,
Sunniva

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continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] Freeview crashes when trying to load volumes

2024-01-15 Thread fsbuild 
External Email - Use Caution

 It would help for us to know what your machine is running, e.g., linux or 
MacOS (Intel or Silicon Mac) - and what the version is for the operating 
system, e.g. Linux Ubuntu 22, MacOS 12, etc.  If you are running Linux on 
Windows thru either WSL or a VM then please mention that and if the Windows 
host is running Win 10 or 11.
- R.
On Jan 12, 2024, at 11:52, Ford, Jamie K  
wrote:External Email - Use 
CautionHello,Please could I get 
some advice on my installation? I've downloaded version 7.4.0 using the same 
steps described in the installation video MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFile&do=get&target=installFS_demo.mp4 Everything
 seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like 
on the video). Freeview then crashes. This is the same for any 
volume. Could someone please advice? Any guidance would be greatly 
appreciated.Many 
Thanks,Jamie___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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