Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 06 Jul '22

06 Jul '22

Dear FreeSurfer team, 1. We are attempting to compute the average cortical thickness for controls and persons with a neurological condition. In some cases, we’ve noticed that the pre- and post-central gyri have shifted in the anteroposterior direction so that the left and right gyri are not aligned. A similar phenomenon has been reported previously (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70316.html) and solved. However, we get the following error when attempting the previously proposed solution: ERROR: Flag -nospherereg unrecognized Are there any other solutions or suggestions for addressing this shift that may work for us? 1. Also, if we are interested in analyzing the cortical thickness of the entire hemispheres using the mri_glmfit-function and not comparing specific ROIs directly, does the correct parcellation/labelling of specific ROIs matter? Kind regards, Carl FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Platform: CentOS Stream 8 Screenshot: please see attached

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Research Technician position available
by Fischl, Bruce 06 Jul '22

06 Jul '22

The NIH-funded MGH Metabolic Imaging Core is seeking to fill a position of full-time Research Technician I role in the field of metabolic imaging. As part of the research group, the incumbent will work in a highly dynamic clinical research environment in metabolism, focused on body composition, obesity, osteoporosis, and lipodystrophy. This is a position in which the incumbent will provide oversight in research imaging used in metabolic imaging and body composition, provide expertise in data analysis and develop tools for imaging acquisition and analysis. The candidate will report directly to the Core Director and/or Lab Manager and have support of imaging technologists. These activities will provide an opportunity for developing mentored research or collaborations, as well as hands-on experience in a clinical environment. Ideal candidates have experience or interest in medical imaging, machine learning, metabolism, human research, biology and/or engineering background. Read more here: https://partners.taleo.net/careersection/ex/jobdetail.ftl?job=3205627&lang=…

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Where to ask for FS72 VM passcode?
by Mikolaj Pawlak 06 Jul '22

06 Jul '22

External Email - Use Caution Hi, Where should one ask for the passcode for FS72 VM passcode for 7-zip file? https://secure-web.cisco.com/11mE0Ia6yDy37AsxgjQk5KAenDuqY2WdhwEC41GxoBEtrW… I asked here but received no answer. thanks, Mikolaj

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Password request for FS_7_2_0_Ubuntu_18_04_06.ova.
by Aria Motamedi 06 Jul '22

06 Jul '22

External Email - Use Caution Hello,I hope this email finds you well. I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z file to be able to expand it. Thank you for your time.

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VM archive password
by Vladimir Zenin 06 Jul '22

06 Jul '22

External Email - Use Caution Dear freesurfer team, Could you, please, provide me the password for your FS_7_2_0_Ubuntu_18_04_06.ova.7z distributive? Thank you in advance! Best regards, Vladimir Zenin

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Standalone freeview
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 05 Jul '22

05 Jul '22

External Email - Use Caution Hi developers, I have some colleagues who have been assigned to quality check brain scans remotely on their laptops (macs), and they have space constraints. Is there a stand alone freeview-only installation that doesn't require the ~10gb needed for the entire freesurfer suite? Sorry if this question has already been asked. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Fwd: Passcode for the VM
by MANUEL RUOCCO 05 Jul '22

05 Jul '22

External Email - Use Caution Hello, I would like to ask for the passcode for the VM file containing FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you for your assistance.

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Postdoc Position in Cognitive Neuroscience at Tulane University
by Ben Deen 05 Jul '22

05 Jul '22

External Email - Use Caution The Social Memory Lab, directed by Dr. Ben Deen, is seeking a Postdoctoral Fellow. The lab studies social perception, cognition, and memory, with the goal of characterizing the cognitive and neural basis or our ability to understand other people. We use behavioral and neuroimaging (fMRI) methods in humans, with a focus on precision imaging of functional organization in individual brains. Specific research projects within that scope are flexible and dependent on the interests of the candidate. Fellows will have the opportunity to conceive of and design research studies, lead and participate in data collection and analysis, mentor graduate and undergraduate lab members, write fellowship and grant proposals, and present their results at scientific conferences. *REQUIRED EDUCATION AND EXPERIENCE:* 1. PhD in psychology, neuroscience, or a related field *REQUIRED KNOWLEDGE, SKILLS, ABILITIES/COMPETENCIES* 1. Ability to communicate effectively with lab members, university staff, and volunteers 2. Experience with behavioral and/or neuroimaging research with human participants 3. Proficiency coding in Matlab, Python, or R *PREFERRED QUALIFICATIONS:* 1. Experience with fMRI data collection and analysis 2. Strong publication record in psychology and/or neuroscience Interested candidates may apply online at http://secure-web.cisco.com/1MoQV-Z4F4SEZC3oVL8Qnleak3C0d8YKf-cog-cSxWXfCBn… or email bdeen(a)tulane.edu with any questions about the position.

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Research Technician Position in Cognitive Neuroscience at Tulane University
by Ben Deen 05 Jul '22

05 Jul '22

External Email - Use Caution The Social Memory Lab, directed by Dr. Ben Deen, is seeking a Laboratory Research Technician who will contribute to multiple aspects of research projects studying social perception, cognition, and memory, using behavioral and neuroimaging (fMRI) methods. The Laboratory Research Technician will work as part of a team comprised of postdoctoral fellows, graduate students, and undergraduate research assistants, and will coordinate day-to-day operations of the lab. Major responsibilities include participant recruitment, collection of behavioral and fMRI data, data analysis using Matlab or Python, and administrative duties. Other tasks will be commensurate with the experience and interests of the technician. The position requires excellent communication and organizational skills, a high degree of independence, and an interest in cognitive neuroscience. *REQUIRED EDUCATION AND EXPERIENCE:* 1. Bachelor’s degree in psychology, neuroscience, computer science, or a related field 2. Previous experience working in a research lab *REQUIRED KNOWLEDGE, SKILLS, ABILITIES/COMPETENCIES* 1. Ability to communicate effectively with lab members, university staff, and volunteers 2. Ability to perform daily tasks in a highly organized fashion, with attention to detail 3. Strong time management skills and ability to effectively manage multiple assignments 4. Willingness to work flexible hours, including evenings and weekends as needed 5. Desire to acquire new skills and competencies in a dynamic research atmosphere 6. Proficiency in computer skills, including Microsoft Office applications *PREFERRED QUALIFICATIONS:* 1. Proficiency coding in Matlab, Python, or R 2. Demonstrated interest in cognitive neuroscience research Interested candidates may apply online at https://secure-web.cisco.com/1wldJZ_Nw3f2XASAdXti-afFK0hYTKcIYRrtzeeaSycTIG… or email bdeen(a)tulane.edu with any questions about the position.

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Freesurfer VM password
by #ATILGAN HICRET# 04 Jul '22

04 Jul '22

External Email - Use Caution Hi, May I have a passcode to the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install free surfer virtual disk ? Best wishes, Hicret

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