Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Re: [Freesurfer] password for FS_Ubuntu_18_04_06.ova
by fsbuild 09 Feb '22

09 Feb '22

External Email - Use Caution Sending to your private email shortly.  Please note that the VM is currently setup to Freesurfer 7.2.0 out of the box. - R. On Feb 9, 2022, at 07:38, Deirel Paz Linares <deirel.paz(a)neuroinformatics-collaboratory.org> wrote:        External Email - Use Caution        Dear mailmanCould you please share with me the password for the user “developer” in the Ubuntu 18.04 Virtual Machine containing Freesurfer 6 “FS_Ubuntu_18_04_06.ova”? Best regards _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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password for FS_Ubuntu_18_04_06.ova
by Deirel Paz Linares 09 Feb '22

09 Feb '22

External Email - Use Caution Dear mailman Could you please share with me the password for the user "developer" in the Ubuntu 18.04 Virtual Machine containing Freesurfer 6 "FS_Ubuntu_18_04_06.ova"? Best regards

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macOS Monterey (Apple Silicon) and macOS Catalina (Intel-based), Freeview keeps crushing
by Kaya, Kutlu 09 Feb '22

09 Feb '22

Hi, I installed FreeSurfer version 7.2.0 via pkg file. FreeSurfer is working fine, but when I try to freeview either via terminal command or directly, it keeps crushing (please see the attached file). I uninstalled and re-install again. This time freeview is opening, but is still crashing. I’m using macOs Monterey with Apple Silicon. Although I’ve tried on macOs Catalina with intel-based, it still crushes. I’m not exactly sure what the problem is. Would you please help for it? Thank you so much! Kutlu

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PhD position in Developmental Cognitive Neuroscience
by Marisa Johanna Nordt 09 Feb '22

09 Feb '22

External Email - Use Caution PhD position in Developmental Cognitive Neuroscience Junior Group Leader Dr. Marisa Nordt in the Clinical Child Neuropsychology Section at RWTH Aachen University Hospital (Aachen, Germany) is currently recruiting a PhD student. Job description Our group is looking for a highly motivated and enthusiastic PhD candidate in the field of Developmental Cognitive Neuroscience. The successful applicant will work in a project investigating the effects of experience on human brain development with a focus on high-level visual perception (for example, perception of faces and written words) using a combination of different methods including (f)MRI and behavioral measures. The position is funded for 3 years and may be extended. Your profile * Master’s degree in Psychology, Biology, Computer Science, Cognitive Science, Neuroscience, or a related discipline * Attention to detail and the ability to work independently, as well as excellent communication and interpersonal skills * Interest in Developmental Cognitive Neuroscience and brain development * Strong statistical and methodological skills and interests * Knowledge of Matlab, Python, R, or a strong motivation to acquire these skills * Fluency in English and at least intermediate levels of German * Experience in working with children is a plus Your tasks * Learn how to design and conduct (functional) MRI studies in children and adults including behavioral assessments and apply advanced techniques to analyze these data * Presentation and publication of the results * Interaction with team members and international collaborators * We are a young, dynamic, and highly motivated team affiliated with the Clinical Child Neuropsychology Section at RWTH Aachen University Hospital, which provides an outstanding research environment with many opportunities for clinical research. Feel free to reach out to Dr. Marisa Nordt (mnordt(a)stanford.edu<mailto:mnordt@stanford.edu>) for more information. Applicants should email a CV, a letter of motivation, the expected date of availability and the names of two references as a single PDF to mnordt(a)stanford.edu<mailto:mnordt@stanford.edu> before March 5th 2022. The start date is negotiable, but earlier start dates are preferred.

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trac-all -prep with intrareg = 2
by Mirro, Amy 08 Feb '22

08 Feb '22

External Email - Use Caution Hello freesurfer devs, Thank you so much for all of your work on Tracula! I have been following this conversation (https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBet…) about an issue using flirt, and I am having a similar issue. It sounds like this user switched to bbregister, and that resolved the problem, but I was hoping to do a quick comparison between flirt and bbregister. I am running on Linux centos7 and my freesurfer build-stamp.txt is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b. When I run trac-all -prep with flirt (setting intrareg = 2) , I get a set of errors of the following format: WARN: Could not open /export/freesurfer/freesurfer-7.2.0/trctrain/hcp/mgh_1010/syn/acomm.flt.prep.trk for reading WARN: Error was: Can not open file I think this is a result of the call the dmri_train (around line 2167 in trac-preproc on the 7.2 branch of your github). This call uses a trklist variable, which is set as follows: (around line 2109) set trklist = `printf $xspace/%s.$reg.prep.trk " $pathlist` Since I am running with flirt, the $reg here gets replaced with flt, so the code starts looking for .flt files inside the trctrain folder. As far as I can tell the trctrain directory only contains .bbr files. Should there be .flt files within this directory? Would it make sense to replace the $reg variable with a hard-coded '.bbr'? Or are the tracks that I should be using with flirt different from those that I should use with bbr? Thanks, Amy <https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBet…> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] VM developer password
by fsbuild 08 Feb '22

08 Feb '22

External Email - Use Caution Sending to your email shortly. - R. On Feb 8, 2022, at 13:11, Dale Pike <dale.pike(a)gmail.com> wrote:        External Email - Use Caution        I understand that this is where I am to request a password to the Ubuntu VM image for the developer account? Please advise.Thanks,Dale_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM developer password
by Dale Pike 08 Feb '22

08 Feb '22

External Email - Use Caution I understand that this is where I am to request a password to the Ubuntu VM image for the developer account? Please advise. Thanks, Dale

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FW: Survey testing experimental setup
by Lepauvre, Alex 08 Feb '22

08 Feb '22

External Email - Use Caution Dear Freesurfer community, Our survey to regarding common practices to test experimental setup will be over soon. If you haven't had time to fill it out just yet, here is the link again. We are looking forward to your responses :) Thanks in advance for your help, Kind regards, Alex From: Lepauvre, Alex Sent: Monday, 31 January 2022 09:11 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: Survey testing experimental setup Dear Freesurfer community, Have you ever wondered what is the impact that the experimental setup might have on reported results in neuroscience and psychology? If yes, you are not alone! We have created a survey to better understand and identify common practices used in the field to test experimental code and experimental hardware. This survey is addressed to anyone having undertaken the programming, implementation and testing of a neuroscientific or psychophysical experiment at some point in their careers. The responses to the survey are anonymized and the data will be presented as aggregates. We aim to collect responses from a wide variety of researchers, hopefully at different career stages. Feel free to share the link with as many of your peers as possible. The survey will take no more than 5 mins to be completed. By clicking on this link, you will proceed to the survey: https://secure-web.cisco.com/1fKDJuWL3IFUkiyyHuSdPDvH7BPDhY3S5gKmEnllfEETXM… Thanks in advance for your help! Kind regards, Alex & Rony Alex Lepauvre, Max Planck institute for empirical aesthetics, Frankfurt, Germany Rony Hirschhorn Tel-Aviv University, Tel Aviv, Israel

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Using -bigventricles for infant segmentation
by Fateme Sadat Haghpanah 07 Feb '22

07 Feb '22

External Email - Use Caution Dear FreeSurfer Developers, I am trying to use the InfantFS segmentation pipeline for segmenting images with Ventriculomegaly. I have looked up the archive and found out the -bigventricles. I have tried the following commands but it did not work. Can you help me to figure out how I can segment these images with infantFS? infant_recon_all -bigventricles --newborn --s ${SUBJ} —> ERROR: Flag -bigventricles unrecognized Regards, Fateme

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PhD position in Cognitive Neuroscience
by Nicolas Langer 07 Feb '22

07 Feb '22

External Email - Use Caution PhD position in Cognitive Neuroscience Department: Department of Psychology at the University of Zurich (Switzerland), Methods of Plasticity Research (http://secure-web.cisco.com/1yrXnmcLak8VcmE09mDHZoci-sk4X3q07igz895-SUBVrvp… <http://secure-web.cisco.com/1yrXnmcLak8VcmE09mDHZoci-sk4X3q07igz895-SUBVrvp…>) Position: PhD student (salary 54’000 USD/year) 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 MRI, 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 the Synapsis-foundation funded research project “Real-life activity tracking as pre-screening tool for early stages of Alzheimer disease”. The aim of the project is to investigate whether real-life activity measures, derived from wearable technology (e.g. GPS and accelerometer data), are sensitive to identify early stages of Alzheimer’s disease. Further, we aim to provide evidence that these real-life activity measures are associated with current AD biomarkers (i.e. high Amyloid level and brain atrophy). The student will be expected to disseminate study results in peer reviewed journals, and to supervise Master’s students. The candidate will work in the team of Prof. Nicolas Langer, who is also part of the Neuroscience Center Zurich (ZNZ) (https://secure-web.cisco.com/1j9dVWlEovAAe9t5FR6nKcRvk_0Yl721sHAUBF-hXb_iJz… <https://secure-web.cisco.com/1j9dVWlEovAAe9t5FR6nKcRvk_0Yl721sHAUBF-hXb_iJz…>), which offers a renowned international PhD programme in Neuroscience. The candidate will work closely with the Institute for Regenerative Medicine (https://secure-web.cisco.com/1c97BxJICcB3NTZIZFQKFhpVHVc-8EJh72iy6rEy22EbOj… <https://secure-web.cisco.com/1c97BxJICcB3NTZIZFQKFhpVHVc-8EJh72iy6rEy22EbOj…>), Geographic Information Systems (https://secure-web.cisco.com/10BeiM-zzcFs3UtSRm8gQk7oMwijYSyO4gQhISpbG9k_m6… <https://secure-web.cisco.com/10BeiM-zzcFs3UtSRm8gQk7oMwijYSyO4gQhISpbG9k_m6…>), University Research Priority Programme from the University of Zurich “Dynamics of Healthy Aging” (https://secure-web.cisco.com/1ES7m6_j-xtuKVPJ2bSeckrMa9dywupWgezD1AphiCY6PO… <https://secure-web.cisco.com/1ES7m6_j-xtuKVPJ2bSeckrMa9dywupWgezD1AphiCY6PO…>), and the Department of Computer Science at the ETH Zurich (https://secure-web.cisco.com/1lxmmD3IZNOWGQgMIQyHgzhT6k-IZxsdYUMVJGdRRZfNTk… <https://secure-web.cisco.com/1lxmmD3IZNOWGQgMIQyHgzhT6k-IZxsdYUMVJGdRRZfNTk…>). Workload %: 80 - 100% Qualifications: · MSc degree in a field related to cognitive neuroscience (e.g., cognitive neuroscience, (neuro-)psychology, computer science, biomedical or electrical engineering) · Deep knowledge in data science (time-series data processing, feature engineering and analysis) · Proficiency in programming (in Python, Matlab or R) is a must · Knowledge in mobile and wearable digital technologies is desirable · Experience with amyloid PET imaging and/or structural MRI analyses are a plus · Training in machine learning is a plus · Excellent verbal and written English skills 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 (54’000 USD/year) and generous social benefits · Employment 3 years with the possibility of extension · Generous support for professional travel and research needs (~3’000 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 (Department of Computer Science (ETH Zurich; Ce Zhang), Institute for Regenerative Medicine (UZH; Prof. Christoph Hock), Geographic Information Systems (UZH; Prof. Robert Weibel) · The opportunity to live in Zurich, one of the world’s most attractive cities Please visit https://secure-web.cisco.com/1Gd2AFC0ba61SE-PzvsUt26JL6je1tQ1bXlro3LofYXN_h… <https://secure-web.cisco.com/1Gd2AFC0ba61SE-PzvsUt26JL6je1tQ1bXlro3LofYXN_h…> for further information. This position opens on: 1.6.2022 (starting date) 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.ch <file:///Users/nickilanger/Dropbox/AA_UZH_ADMIN/wichtige_dokumente%20&%20HR/Ausschreibung_PostDoc/n.langer@psychologie.uzh.ch> Applications will be considered until the position is filled (ideally submit your application before 31st of March 2022). Description of the Project: Real-life activity tracking as pre-screening tool for early stages of Alzheimer disease Alzheimer's disease (AD) accounts for the majority of all dementia cases and represents a major and rapidly growing burden to the healthcare and economical systems. The current state of research indicates that therapies need to be administered as early as possible. Therefore, there is an urgent need for accelerating biomarker discovery for early stages of AD. Importantly, evidences suggest that neurodegenerative changes precede clinical manifestations of AD by 20-30 years. However, prevailing potential biomarkers for early stages of AD diagnosis, including genetic testing, molecular examination of CSF, structural MRI and PET imaging, are highly limited as they can only be applied to relatively small sample sizes due to their excessive costs and invasive nature. This prevents their usage in large epidemiological studies; yet such study designs are imperative for identifying the intra-individual progression from healthy ageing to AD. Thus, novel non-invasive and inexpensive biomarkers are urgently required to be administered at large scale with the aim to identify individuals with indications for early stages of AD. These identified subjects could then be referred to undergo more cost-intensive examinations with the currently available biomarker techniques to achieve the desired diagnostic accuracy. Mobile and wearable digital technologies have an unprecedented potential and could close this current gap as they permit abundant, continuous longitudinal data acquisition at low costs to investigate intra-individual changes as early markers of AD. In this project, we will investigate whether activity measures, derived from GPS and accelerometer data, are sensitive to identify early stages of AD (i.e. mild neurocognitive disorder due to AD). Further, we aim to provide evidence that real-life activity measures are associated with current AD biomarkers (i.e. high Amyloid level and brain atrophy). Because our long-term vision is to develop a smartphone application that is able to identify intra-individual trajectories in healthy adults to establish the transition point to mild neurocognitive disorder due to AD as early as possible, we will examine the sensitivity of the real-life activity measures for intra-individual changes. Therefore, the present proposal serves as a proof-of-concept to address the prerequisites for real-life activity tracking as a pre-screening assessment tool to identify potential mild neurocognitive disorder patients. Nicolas Langer 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/1eprtfu6YVQ2Y3Wfp5VzOWnZz0Gm19H1RYpdVB_ZXOnH9Gb…

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