Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Re: [Freesurfer] Pass code virtual box
by fsbuild 29 May '22

29 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 27, 2022, at 14:33, Max Hinrichs <hinrichs-max(a)web.de> wrote:        External Email - Use Caution        Hi,  I downloaded the FreeSurfer virtual box (https://secure-web.cisco.com/10EIfghQmCyH4hbcuz3ZyZ_H2_2dnkYSuUFkHCdmUoW5pi…) and wanted to ask whether you can send me the pass code. Best wishes, Max _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Using Freesurfer package in MLOps framework
by fsbuild 29 May '22

29 May '22

External Email - Use Caution Hello, The package and associated dependency tools that are part of an existing Linux OS use either the freesurfer .rpm (Redhat, CentOS, etc.. linux derivatives) or the .deb package file (Ubuntu, Debian, etc. linux derivatives) to dynamically determine what (if any) dependent packages need to be installed on the target linux system based upon the dependencies in the freesurfer package file.  Those dependencies are derived from the symbol versions compiled into the freesurfer binaries.  The point of using the .rpm or .deb installer files with the native linux system yum, rpm, dpkg, apt, etc. tools is so no one has to manually figure out the freesurfer dependencies - which could be different on any given linux system.   If you don’t have root/sudo privileges to install the .rpm or .deb files on a linux system, then you can unarchive the .tar.gz file (which provides no dependency checking).   You can see all the available packages for the current 7.2.0 release at https://secure-web.cisco.com/1uYwfyUWWoTgl9ozxMEZNw1QqBdCnOmN1uHLFI… - R. On May 29, 2022, at 03:57, 우앙청심환 <dlagudduf13(a)gmail.com> wrote:        External Email - Use Caution        Hi, I'm using a program based on the MLOps framework and just want to use the Freesurfer package in this. but I found the only installable file on the document page.so what I would like to ask is, is it possible to install and use the freesurfer package separately in an environment such as Google Colap, in addition to the existing method of extracting and installing freesurfer on Linux.. If possible, I wonder what is the dependency of the freesurfer package..Best regards.  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Using Freesurfer package in MLOps framework
by 우앙청심환 29 May '22

29 May '22

External Email - Use Caution Hi, I'm using a program based on the MLOps framework and just want to use the Freesurfer package in this. but I found the only installable file on the document page. so what I would like to ask is, is it possible to install and use the freesurfer package separately in an environment such as Google Colap, in addition to the existing method of extracting and installing freesurfer on Linux. If possible, I wonder what is the dependency of the freesurfer package. Best regards.

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Re: [Freesurfer] Unable to install Matlab runtime to run the SegmentHA function in Mac OS 12.4
by fsbuild 28 May '22

28 May '22

External Email - Use Caution Try running the install with sudo, e.g., $ sudo fs_install_mcr  R2014b If that does not work, you could try turning off the gatekeeper on MacOS (although this weakens your system security), and then see if the install works. $ sudo spctl --master-disable … then to re-enable the gatekeeper, $ sudo spctl --master-enable On May 26, 2022, at 23:18, Isabella Leung <I.Leung(a)westernsydney.edu.au> wrote:<Terminal screenshot.jpg>

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Postdoctoral Research Fellow in New York – MR correlates of Gait and Falls in multiple sclerosis
by Mark Wagshul 27 May '22

27 May '22

External Email - Use Caution Postdoctoral Research Fellow in New York – MR correlates of Gait and Falls in multiple sclerosis A postdoctoral research fellow position is available immediately in the departments of Radiology and Neurology at the Albert Einstein College of Medicine in NY. The goal of our NIH-funded project (Brain predictors of mobility and falls in older adults with multiple sclerosis - 5R01NS109023) is to investigate the structural and functional brain correlates of gait impairment and falls in older multiple sclerosis patients. Using innovative statistical modeling methods allowing us to draw inferences from walking data (functional near-infrared spectroscopy during complex walking tasks) combined with advanced structural and functional imaging data, the project aims to elucidate the brain pathways involved in cognitive control of walking, and their relationship to risk of falls, and how these pathways are affected in elderly MS patients. We currently have collected data structural and/or functional MRI methods (e.g. DTI/NODDI, rs-fMRI) on > 150 patients and controls, an extremely rich dataset which will be available to the research fellow for data analysis, manuscript generation and exploring new data and modeling approaches to these data. We are seeking a highly-motivated individual with experience in neuroimaging analysis methodologies. Candidates should have: - PhD in BME, physics, computer science, cognitive neuroscience or related disciplines, - Experience with structural and/or functional MRI data analysis (e.g. NODDI, rs-fMRI). - Solid programming background (e.g., FSL, SPM, Freesurfer, Matlab) - Comfortable with data analysis in a Linux environment. - Familiarity with computational and statistical methods related to imaging analyses. A strong work ethic, excellent organizational and communication skills is expected as well as the ability to work in an interdisciplinary environment. Willingness to learn new techniques or software environments and a strong foundation in neuroanatomy is plus. Writing experience, a good publication record, and the ability to work independently will be strongly favorable. The Albert Einstein College of Medicine is a leading academic institution, with over $170M in NIH funding. The candidate will have access to state-of-the-art brain imaging (3T MRI) and computing facilities. Einstein is one of the nation’s premier institutions for medical education, basic research and clinical investigation. It is home to some 2,000 faculty members, 750 M.D. students, 350 Ph.D. students attending the Sue Golding Graduate Division — including 125 in the combined M.D./Ph.D. program — and 325 postdoctoral investigators training at our Belfer Institute for Advanced Biomedical Studies. More than 7,000 Einstein alumni are among the nation’s foremost clinicians, biomedical scientists and medical educators. Interested candidates should send their CV, a brief statement of their research interests and career goals, and the names and contact info of three references to Mark Wagshul (mark.wagshul(a)einsteinmed.edu) Review of applications will begin immediately and continue until the position is filled. The Albert Einstein College of Medicine is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, protected veteran or disabled status, or genetic information. Einstein seeks candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence, and the communities we serve. ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Pass code virtual box
by Max Hinrichs 27 May '22

27 May '22

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2 Postdoctoral Positions in Cognitive Neuroscience of Visual Memory, Aging, and Alzheimer’s disease at Brown University
by Sharp, Elizabeth 27 May '22

27 May '22

External Email - Use Caution *Postdoctoral Positions in Cognitive Neuroscience of Visual Memory, Aging, and Alzheimer’s disease* Category: Postdoctoral Position Area: Cognitive and Translational Neuroscience Department: Depts. of Psychiatry and Human Behavior and Cognitive, Linguistic, and Psychological Sciences Institution: Brown University We are seeking two highly motivated postdoctoral researchers to lead NIH-funded projects in the Laboratory for Cognitive and Translational Neuroscience directed by Dr. Hwamee Oh at Brown University. One position is to use fMRI and PET to study visual memory networks in healthy young, cognitively normal older adults, and older adults who are considered as preclinical Alzheimer's disease. The other position is to understand the individualized brain networks that are affected by Alzheimer’s disease pathology among non-demented older adults. Applicants with a Ph.D. degree in cognitive neuroscience, computational neuroscience, biomedical engineering, or a relevant field are encouraged to apply. Prior experience with human neuroimaging, a strong background in cognitive neuroscience and experimental design, and/or familiarity with programming in relevant languages (e.g., Python, MATLAB) are required. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive and brain aging, Alzheimer’s disease, and neuroimaging, and the ability to independently develop research questions and work in collaboration with other team members. The expected start date is fall 2022 or negotiable. Interested applicants should email a brief description of research background and career goals, and CV with a list of 3 references to Dr. Hwamee Oh at hwamee_oh(a)brown.edu. Contact Website https://secure-web.cisco.com/1FVngwkuBiIfTQ_58cdg0C6ODiG0OHOdjp-IkNW2C7EAs7… -- Elizabeth Sharp Research Assistant Oh Lab Brown University

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Re: [Freesurfer] Unable to install Matlab runtime to run the SegmentHA function in Mac OS 12.4
by fsbuild 27 May '22

27 May '22

External Email - Use Caution Hello Isabella, Please try running the matlab install script that is provided in the freesurfer distribution with, $ fs_install_mcr  R2014b - R. On May 26, 2022, at 23:18, Isabella Leung <I.Leung(a)westernsydney.edu.au> wrote:        External Email - Use Caution        Hello Freesurfer expert,I have installed Freesurfer 7.2.0 onto my personal Mac OS (Monterey 12.4). The Recon-all function works but when I try to run the segmentHA_T1.sh bert  [SUBJECTS_DIR]It tells me to install the Matlab R2014b runtime. I have downloaded and installed Matlab R2014b but it still tells me that I need to install the "runtime".I have downloaded the "MCR_R2014b_maci64_installer" but it gets stuck when I try to install and won't let me get past the libjvm.dylib no matter how many times I click the "Allow Anyway" button in my system preferences. I'm not sure what to do. Is there a script that I can run that will allow me to install the matlab runtime without being blocked or is there another script that will allow me to run the Segment HA without the matlab runtime installed? Many thanks and looking forward to hearing from you.Best wishes,IsabellaIsabella LeungPost-Doctorate Fellow in Clinical ResearchNICM Health Research Institute, Western Sydney Universitye.     i.leung(a)westernsydney.edu.au    p.     +61 403 234 141       w.     nicm.edu.auNICM Health Research Institute is an initiative seeded by the Australian and NSW Governments at Western Sydney UniversityUnit Coordinator for Evidence-Based Practice in Chinese Medicine School of Health Sciences, Western Sydney Universitye.   i.leung@westernsydney.edu..au   p.     +61 403 234 141   w.     MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1iDu9RElIk3CllbWjTZq1l5YjpqejiK3mOT4S… screenshot.jpg><Runtime installer screenshot.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] pass code to open ubuntu image for windows
by fsbuild 27 May '22

27 May '22

External Email - Use Caution Sending the info to your email shorty. - R. On May 23, 2022, at 11:17, Juan Ruiz de Miras <demiras(a)ugr.es> wrote:       External Email - Use Caution        Hi,Following the instructions on your web page, with this email I ask you for the pass code to open the freesurfer ubuntu image for windows.Regards,Juan._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Unable to install Matlab runtime to run the SegmentHA function in Mac OS 12.4
by Isabella Leung 26 May '22

26 May '22

External Email - Use Caution Hello Freesurfer expert, I have installed Freesurfer 7.2.0 onto my personal Mac OS (Monterey 12.4). The Recon-all function works but when I try to run the segmentHA_T1.sh bert [SUBJECTS_DIR] It tells me to install the Matlab R2014b runtime. I have downloaded and installed Matlab R2014b but it still tells me that I need to install the "runtime". I have downloaded the "MCR_R2014b_maci64_installer" but it gets stuck when I try to install and won't let me get past the libjvm.dylib no matter how many times I click the "Allow Anyway" button in my system preferences. I'm not sure what to do. Is there a script that I can run that will allow me to install the matlab runtime without being blocked or is there another script that will allow me to run the Segment HA without the matlab runtime installed? Many thanks and looking forward to hearing from you. Best wishes, Isabella Isabella Leung Post-Doctorate Fellow in Clinical Research NICM Health Research Institute, Western Sydney University e. i.leung(a)westernsydney.edu.au<mailto:i.leung@westernsydney.edu.au> p. +61 403 234 141 w. nicm.edu.au<http://secure-web.cisco.com/1uOIvmC0uTfFg7SmaAz1IwHOiK7TEnE6msNrSYrR-CH8p-c…> NICM Health Research Institute is an initiative seeded by the Australian and NSW Governments at Western Sydney University Unit Coordinator for Evidence-Based Practice in Chinese Medicine School of Health Sciences, Western Sydney University e. i.leung(a)westernsydney.edu.au<mailto:i.leung@westernsydney.edu.au> p. +61 403 234 141 w. https://secure-web.cisco.com/1KD9C7FKKxu6CkI2KpA6OrtwoHRvxhZbQcTrrNzA4M12bC… ________________________________ [200106_N_Western_email_sig]

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