Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

Usage of embedded colors in Freeview tract visualizer + anatomicuts error
by Pietro Astolfi 04 Jan '21

04 Jan '21

External Email - Use Caution Hi, In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online. I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6 If anyone could help me it would be very appreciated, Best, Pietro Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology -- -- Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.

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Re: [Freesurfer] Ubuntu Login FreeSurfer {Disarmed}
by fsbuild 04 Jan '21

04 Jan '21

External Email - Use Caution Sending this along to your posted email. - R. On Jan 4, 2021, at 08:41, Dimitri Brigide De Almeida Mantovani <dimitri.brigide(a)edu.pucrs.br> wrote:        External Email - Use Caution        I am attempting to start Ubuntu via VirtualBox on Windows 10, but  Ubunturequests a login password for the "Developer" account, while installationguide assumes automatic login. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu Login FreeSurfer
by Dimitri Brigide De Almeida Mantovani 04 Jan '21

04 Jan '21

External Email - Use Caution I am attempting to start Ubuntu via VirtualBox on Windows 10, but Ubuntu requests a login password for the "Developer" account, while installation guide assumes automatic login.

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tkregister-sess: no windows pop up
by Kazuhisa Shibata 04 Jan '21

04 Jan '21

External Email - Use Caution Dear the developers. I have been trying to check the quality of registration between functional and structural images by using tksurfer-sess. Although it says “tkregister-sess completed”, no windows pop up. I have confirmed that Xquartz is working (xclock shows the clock). I’d be extremely grateful if you could give me your advise on this. For your reference, I have attached a log file and showed what was displayed on the terminal below. I use Mac OS11.1. Best, Kaz -- Kazuhisa Shibata Team Leader Lab for Human Cognition and Learning Center for Brain Science RIKEN https://secure-web.cisco.com/1_DTkcMx0GtpUOQXiw7nzTp30ywRlb3dnZPqeNvkA-BtbU… kazuhisa.shibata(a)riken.jp kazuhisa.shibata(a)gmail.com

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Postdoctoral position available at University of Zurich {Disarmed}
by Nicolas Langer 04 Jan '21

04 Jan '21

External Email - Use Caution Postdoctoral Researcher in multimodal Cognitive Neuroscience Department: Department of Psychology at the University of Zurich (Switzerland), Methods of Plasticity Research (http://secure-web.cisco.com/15xs8lafg346k_c6wQpJcwHi5NbuB91HHcB7Mh3fiffomoM… <http://secure-web.cisco.com/15xs8lafg346k_c6wQpJcwHi5NbuB91HHcB7Mh3fiffomoM…>) Position: Postdoctoral Researcher (salary 98’000 USD/year; funding 2 years with the possibility of extension) Description of UZH unit: Our lab develops novel methodological approaches to study variations in cognitive performance across the lifespan and along the continuum from healthy to pathological functioning. Specifically, we investigate the potential for plasticity, mechanisms for stabilization and compensation across the lifespan. For this, we acquire and analyze multimodal data sets, such as structural MR, diffusion weighted data (DWI), simultaneous EEG and eye-tracking as well as behavioral data. From these rich data sets, we extract multivariate parameters and apply state-of-the-art methods, such as machine learning, functional network modelling, and longitudinal analyses. Responsibilities: The successful candidate will work on research in large scale multimodal projects to predict future cognitive decline from multimodal brain imaging data and non-brain risk factors (see project description below). Main responsibilities include the analysis of structural MRI data (optionally also DWI data), dissemination of study results in peer reviewed journals, and the supervision of PhD and Master students. The candidate will take part in ongoing projects and initiate new research within the team of Prof. Nicolas Langer, who is also part of the Neuroscience Center Zurich (ZNZ) (https://secure-web.cisco.com/1kWQrgNyOKlB698jUbZJqq5RXtC39CWSD5FzuX2fEEsgz_… <https://secure-web.cisco.com/1kWQrgNyOKlB698jUbZJqq5RXtC39CWSD5FzuX2fEEsgz_…>), closely collaborating with the University Research Priority Programme from the University of Zurich “Dynamics of Healthy Aging” (https://secure-web.cisco.com/1RRmvZnMpUoqm2bygZYZYg77v-eQzkTSubTilO9Zzck_oY… <https://secure-web.cisco.com/1RRmvZnMpUoqm2bygZYZYg77v-eQzkTSubTilO9Zzck_oY…>), the Healthy Brain Network of the Child Mind Institute (US), (http://secure-web.cisco.com/1yB3eGvnDx-1QRbRjfCSV8Qs85AX9uCvIRtLdhwAJxxfAic…) <http://secure-web.cisco.com/1yB3eGvnDx-1QRbRjfCSV8Qs85AX9uCvIRtLdhwAJxxfAic…> and the Department of Computer Science at the ETH Zurich (https://secure-web.cisco.com/1LjuchigmW2wUAE8FGpv5O6mwlo6fMDfxUQDBT4HkWEezV… <https://secure-web.cisco.com/1LjuchigmW2wUAE8FGpv5O6mwlo6fMDfxUQDBT4HkWEezV…>). Workload %: 80 - 100% Qualifications: · PhD degree in a field related to cognitive neuroscience (e.g., cognitive neuroscience, (neuro-)psychology, computer science, biomedical or electrical engineering) · Expertise in structural MRI analyses is a must · Proficiency in programming in Python is a must (Matlab or R is a plus) · Proficiency in machine learning (e.g. random forest regression models) · Experience with DWI analysis is desirable · Knowledge in resting state fMRI is a plus · Excellent verbal and written English skills · Interest in teaching about methods (e.g. applications of machine learning in neuroscience) Language requirements: English We offer: · To work in a team of highly motivated young researchers who are passionate about neuroscience, psychology and computer science · A very competitive salary (98’000 USD/year) and generous social benefits · Employment 2 years with the possibility of extension · Generous support for professional travel and research needs (~5’000 USD/year) · An inspiring work environment within the Department of Psychology and the University of Zurich and part of the Neuroscience Center Zurich (ZNZ) with many high-caliber collaborations (Frontlab, ICM, Paris, France; University of Montreal, Canada; University of Texas at Austin, USA; Neurospin, Saclay, France) · The opportunity to live in Zurich, one of the world’s most attractive cities Please visit https://secure-web.cisco.com/19xE4ZhEn7jayxIStKf9VEPwNUoG5kLL4yNZ3Mwv9d33IZ… <https://secure-web.cisco.com/19xE4ZhEn7jayxIStKf9VEPwNUoG5kLL4yNZ3Mwv9d33IZ…> for further information. This position opens on: 1.3.2021 (earliest, starting data is flexible) More information: Prof. Nicolas Langer, n.langer(a)psychologie.uzh.ch Application To be considered please stick to the following application format: · CV including publication list and contact details of two referees (max. 3 pages) · Statement describing motivations, personal qualifications and research interests (max. 2 pages) · Save application in one single pdf file with the file name “Methlab_[SURNAME]_[name].pdf” · Send application by email to: n.langer(a)psychologie.uzh Applications will be considered until the position is filled (ideally submit your application before 31st of January 2021). Description of the Project: Predicting future cognitive decline from non-brain risk factors and multimodal brain imaging data The present project aims to develop a framework to predict individual future cognitive decline in healthy and pathological aging based on existing data from multimodal neuroimaging and non-brain risk factors like demographics, baseline cognitive state, health, health behaviors, and genetic (i.e. APOE) data. The project will use data from the Open Access Series of Imaging Studies (OASIS-3) database (oasis-brains.org) and the Alzheimer's Disease Neuroimaging Initiative (ADNI) (http://secure-web.cisco.com/11XJtFz5YDFEahYeH4GEt0HXu4r9pEumlhnJUIyxqrkf6-F…) This databases provides longitudinal data from multiple neuroimaging and risk factor data sources, allowing to characterize cognitive decline over multiple years in healthy and pathological aging in a large sample of over 1’000 participants. The multimodal neuroimaging and risk factors, from the baseline session will be used to predict cognitive decline at follow-up sessions via predictive models. The pilot experiment suggests that a combination of non-brain and structural data give the best predictions of future cognitive decline. The model needs to be refined by benchmarking different data processing strategies for input and further improving the generalizability by increasing the model’s robustness against site-effects. Nicolas Langer Assistant Professor of Methods of Plasticity Research University of Zurich Andreasstrasse 15 (Office AND.4.56) 8050, Zurich, Switzerland n.langer(a)psychologie.uzh.ch phone: (+41) 44 635 34 14 http://secure-web.cisco.com/1xJjzGTaPUnVagGiJnqo9hS-Q5Toeip8e5SwXZuj8rnsDKq…

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talairach.lta coordinate spaces
by Tisdall, Dylan 03 Jan '21

03 Jan '21

External Email - Use Caution Hi list, I'm trying to understand whether the talairach.lta transform is from the image-axes RAS to talairach or the scanner-axes RAS to talairach. Basically, if I rotate the imaging FOV and scan the same subject, should I expect that to change talairach.lta or not? My confusion stems from the discrepancy between what the scanner terms RAS coordinates (aligned to the gradient axes) vs. what might be plausibly called RAS in the image coordinates (aligned to the FOV axes). The underlying goal here is to try to evaluate how gradient-axis-aligned someone's head was when they were loaded in the scanner. Thanks, Dylan --- Dylan Tisdall, PhD Research Assistant Professor Department of Radiology Perelman School of Medicine University of Pennsylvania Room D406 Richards Medical Labs 3700 Hamilton Walk Philadelphia, PA 19104

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Re: [Freesurfer] error in running tkregisterfv (Greve, Douglas N., Ph.D.)
by Peter de Best 03 Jan '21

03 Jan '21

External Email - Use Caution Dear Dr. Greve, Thank you so much for the information. However, after adjusting the registration file to *.lta, I get the same error message. It will probably help me correctly coregister func & anat in the future, but the issue seems more likely to be connected to some setting that I cannot seem to find... Do you have any suggestions/ tips? Best regards (and happy new year), Peter

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Access to datasets used for validation of sbTIV and eTIV measures
by Erus, Guray 03 Jan '21

03 Jan '21

External Email - Use Caution Hello FreeSurfer Developers, I'm working on the validation of a method that calculates ICV. The wiki pages on eTIV and sbTIV: https://secure-web.cisco.com/1NfwRceKeD3VTf9pMcEK-JbxIvMnSdQdPlMoLFc8Asj7-1… https://secure-web.cisco.com/1NnGHZWJ6QIknzbA50Q86PSKxQrceCNCSBmR1j4U6EVMlc… include very useful information related to my work. These pages refer to 2 datasets (SASHA and ADNI30) with manual ICV masks. The text also indicates a path for one of these datasets: "... These subjects are found in /space/freesurfer/subjects/atlases/SASHA ..." If I understand correctly, this is a local/restricted path that is not publicly available. Is that correct? Is there a way I can get access to these datasets for my validation experiments? Thank you and happy new year! Guray Guray Erus, PhD Senior Research Investigator Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Richards Building 3700 Hamilton Walk, 7th Floor Philadelphia, PA 19104

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segmentation fault
by Wei Koo 03 Jan '21

03 Jan '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon2 for a number of subjects, but one of my subjects I get the following error when I run the mri_tesellate command: Removing intersections Segmentation fault FreeSurfer version: freesurfer-darwin-macOS-7.1.1.

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Question about a feature introduced in FS 7.0
by Aaron Tanenbaum 03 Jan '21

03 Jan '21

External Email - Use Caution I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used? Aaron Tanenbaum

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Freesurfer January 2021