Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] consulting about quality of our freesurfer data
by Hale Yapıcı Eser 13 Apr '22

13 Apr '22

External Email - Use Caution *Hale Yapıcı Eser, M.D., Ph.D.* Associate Professor of Psychiatry Koç University School of Medicine Koç University Hospital Department of Psychiatry Maltepe Mh. Davutpaşa Cd.No:4 Topkapı 34010 İstanbul /Türkiye Phone:+90.850.250 8 250 (ext: 29779) http://secure-web.cisco.com/1P0SHuqn5tClskEuGRWxFVPfEOOAvzm9_aGv6V0h8P7BhD8… http://secure-web.cisco.com/1zW0vtWd8meYiJ2d8vZv5yZ5BYk_2tH8yMJfS_Uxt-vlP4b… On Wed, Apr 13, 2022 at 1:43 PM Hale Yapıcı Eser <hyapici(a)ku.edu.tr> wrote: > Dear Allison, > I hope that this email finds you well. I am writing you this email > regarding the help that we need about our freesurfer data. I am the > principal investigator of a research lab at Koç University, Turkey. We are > currently running the freesurfer pipeline, however we need to consult for > some of the data that we have. > I wonder if your team provides a one-to-one consultation for 1 or 2 hours, > and if there is such an option, what would be the cost? > We would be grateful if you could guide us on this. > Looking forward to hearing from you, > All the best > > *Hale Yapıcı Eser, M.D., Ph.D.* > > Associate Professor of Psychiatry > > Koç University School of Medicine > > > > > Koç University Hospital > > Department of Psychiatry > > > > > > > > Maltepe Mh. Davutpaşa Cd.No:4 > > Topkapı 34010 İstanbul /Türkiye > > Phone:+90.850.250 8 250 (ext: 29779) > > > http://secure-web.cisco.com/1P0SHuqn5tClskEuGRWxFVPfEOOAvzm9_aGv6V0h8P7BhD8… > > http://secure-web.cisco.com/1zW0vtWd8meYiJ2d8vZv5yZ5BYk_2tH8yMJfS_Uxt-vlP4b… > > > > >

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Job posting: SRA at UCSD
by Wang, Xin 13 Apr '22

13 Apr '22

External Email - Use Caution Hi there, Could you help to post this job advertisement for our lab as below, please? Thank you so much. Please let me know if you need more. Best, Xin Wang Imaging Researcher This position will work a hybrid schedule which includes a combination of working both onsite and remote. DESCRIPTION The research project will involve multiple neuroimaging studies examining biomarkers of brain aging and dementia. These studies will be partially conducted in collaboration with the UC San Diego Shiley-Marcos Alzheimer’s Disease Research Center. These studies will employ structural, diffusion and contrast MRI, amyloid and tau PET, neuropsychological testing, and blood and/or CSF biomarkers, among other tools, to better understand how brain microstructure, vascular integrity, and neuropathology, relate to disease risk and cognitive decline in Alzheimer’s disease or related dementias. Under the supervision of the project PIs (Drs. Reas and Banks), the incumbent will serve as a research project associate for multiple research protocols assessing neuroimaging biomarkers of dementia. Incumbent is responsible for organizing and managing brain imaging research data. Incumbent will manage Linux based workstations for post processing/data manipulation, and data analysis as well as create, maintain and update research databases. Provide support in project administration and publication preparation of imaging research. May provide assistance and have direct communication with subjects and families involved in research projects. MINIMUM QUALIFICATIONS · Bachelor's degree (psychology, neuroscience, biology, cognitive science, statistics, computer science or related field preferred) or equivalent work experience. · Proven knowledge of human subjects research policies and procedures. Knowledge of the human subject consent process, and federal government regulations pertaining to consenting of subjects. On-line training certificate (acquired on job). Knowledge of IRB, and sponsored research requirements. · Experience in a clinical trials research environment including basic understanding of persons with dementia, preferred experience with MRI in order to recruit, schedule, and test patients for clinical study subjects. · Thorough working knowledge of medical and scientific terminology. · Knowledge of statistical analysis of quantitative brain imaging data measures using SPSS, Matlab, and other statistical programs and prefer skills in coding. · Strong experienced with computers (Personal computer and Macintosh). Skill with personal computers, word processing, spreadsheet, e-mail software, databases, etc. Specifically Linux OS and the Microsoft office suite (excel, access, powerpoint, word, etc). · Proven ability to determine sources of clinical data, analyze the data and information obtained, in order to create documents and to propose solutions to issues and to help in developing standardized operational procedures. · Proven ability in researching clinical data in preparation for grant applications and technical manuals, staying abreast of new research developments. Ability to abstract information from protocol and investigator brochure, which requires summarizing large quantities of data. · Skill in assembling written narrative information using word processing software for documenting image analysis procedures and tracking data. · Excellent interpersonal skills with the ability to use tact and diplomacy with subjects (including patients with cognitive impairment), their families, faculty and institutional staff, as well as when representing the agency in the community. · Ability to collaborate and communicate effectively and diplomatically at all organizational levels, both verbally and in writing. Ability to work professionally and effectively with a diverse population, including the business community, academicians, staff and students. · Excellent record keeping, database management, detail oriented, logical, methodological approach to problem solving, strong process orientation, strong administrative and organizational skills with demonstrated ability to prioritize assignments, maintain workflow, and work productively in meeting critical deadlines and milestones. PREFERRED QUALIFICATIONS · Working knowledge of UCSD Human Research Protections Program policies and Procedures. SPECIAL CONDITIONS · Employment is subject to a criminal background check and pre-employment physical. If anyone is interested in this position, you could contact Dr. Reas (ereas(a)health.ucsd.edu<mailto:ereas@health.ucsd.edu> ) and Dr. Banks(sbanks(a)health.ucsd.edu<mailto:sbanks@health.ucsd.edu> ) for further detail.

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Postdoctoral Researcher in Neuroimaging at Karolinska Institute, Stockholm, Sweden
by Joana Braga Pereira 12 Apr '22

12 Apr '22

External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Associate Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The fellow is expected to be independent, develop his or her own projects, supervise students and show an interest in approaches based on graph theory. In addition, he/she will have the opportunity to develop new skills, analyze large datasets, apply for grants and develop a wide network of collaborations. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, neuropsychology, physics, statistics or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with structural MRI, DTI, fMRI or PET imaging analyses; - Clinical or research experience with aging and/or neurodegenerative disorders. - Excellent record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. To apply please go to: https://secure-web.cisco.com/1_02gjVybcT6ODyv8ExuxWUpg_0WuTiWWNMhc561CKQhUu… <https://secure-web.cisco.com/1BWNMr2dp7URFelZIl8NRiChBwHke1TRTjwurTtb4ITDZl…> (Deadline: 29/04/2022) For further information or general inquires, please contact Joana B. Pereira at jbragapereira(a)gmail.com or joana.pereira(a)ki.se. Best wishes, Joana

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Re: [Freesurfer] Pass code
by fsbuild 12 Apr '22

12 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 12, 2022, at 04:33, Wei <wuhanweizh(a)163.com> wrote:        External Email - Use Caution        Dear professors,I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve.. Would you please send me the pass code for help?wzh _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Pass code
by Wei 12 Apr '22

12 Apr '22

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve. Would you please send me the pass code for help? wzh

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Pass code for FreeSurfer VitrualBox VM Images
by Wei 12 Apr '22

12 Apr '22

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve. Would you please send me the pass code? wzh

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Re: [Freesurfer] Request passcode VirtualBox image archive
by fsbuild 11 Apr '22

11 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 10, 2022, at 05:36, Caterina Trainito <caterina.trainito(a)synlab.it> wrote:        External Email - Use Caution        Hello,I would like to request the passcode for the VirtualBox image archive "FS_7_2_0_ubuntu_18_04_06.ova.7z", as described in the wiki page: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/VM_67Thank you!Best regards,Caterina Trainito, MScResearcherIRCCS Synlab SDNVia Gianturco 113 / Via Brin 55, Naples, Italy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[IMPORTANT MESSAGE] Subfields & MCR problems solved
by Iglesias Gonzalez, Juan E. 10 Apr '22

10 Apr '22

Dear all, We have recently fixed two problems in the subfield modules using the Matlab runtime: 1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS. 2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this). Kind regards, Juan Eugenio Iglesias http://www.jeiglesias.com

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Request passcode VirtualBox image archive
by Caterina Trainito 10 Apr '22

10 Apr '22

External Email - Use Caution Hello, I would like to request the passcode for the VirtualBox image archive "FS_7_2_0_ubuntu_18_04_06.ova.7z", as described in the wiki page: https://secure-web.cisco.com/18CS92dSpHzbEbaM7FWv6m5pnsisNkx8qwe4hCCmONAupm… Thank you! Best regards, Caterina Trainito, MSc Researcher IRCCS Synlab SDN Via Gianturco 113 / Via Brin 55, Naples, Italy

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recon-all error
by cooperr1＠student.unimelb.edu.au 09 Apr '22

09 Apr '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I've also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper

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