Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

problem about PVC of PETSurfer {Disarmed}
by qianqiansci 17 Nov '20

17 Nov '20

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not enough, it made the SUVr of hippocampal subfield we get is not accurate. So we want to use the PVC function of PETSurfer. Whether the PETsurfer output the result of PET image after PVC ? so that we can use it directly to registering with MRI image. If it doesn't output the result, can we save it in some ways? Thank you for your guidance. | | qianqiansci | | qianqiansci(a)163.com | 签名由网易邮箱大师定制

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distance between two vertices in Freeview
by Nasiriavanaki, Zahra 17 Nov '20

17 Nov '20

Dear Freesurfer experts Hi I was trying to measure the dimensions of a surface ROI in a flatten map on Freeview. I used the 3D scale bar to measure the longest diameter of the ROI. My question is how the scale bar is calculating the distance between the two points? Is it the euclidean distance between the two vertices? I calculated the euclidean distance in matlab between the two vertices (using their x and y coordinates) , and the number I get, is much higher than what I see in freeview. I wonder why this discrepancy is happening? I appreciate if you could please let me know the answer to my question. Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Postdoctoral Fellowship in Cognitive Neuroscience - Braga Lab @ Northwestern University {Disarmed}
by Ania Holubecki 17 Nov '20

17 Nov '20

External Email - Use Caution We are seeking a postdoctoral fellow to join the Braga Lab ( https://secure-web.cisco.com/1HqJOdOxFbbEvFFuelHbM7FlG-fov0-xk1W0oKrv-pXwn-…) in the Department of Neurology at the Northwestern University Feinberg School of Medicine. Under the mentorship of Rodrigo M. Braga, PhD, the lab uses and develops neuroimaging techniques to characterize brain network organization and function at the level of individuals. Research topics include the nature of brain regional specialization for language, recollection and mental imagery, as well as the mechanisms of cross-network interaction at high spatiotemporal resolution. Fellows will assist with ongoing research studies using methodologies including functional magnetic resonance imaging (fMRI), intracranial electroencephalography (iEEG) and brain stimulation. Fellows will have opportunities to participate and lead in data collection and analysis, mentorship of students and staff, presentations at national meetings, and writing publications. Requirements: Applicants must have a PhD (or equivalent doctoral degree) in neuroscience or a related field, from an accredited institution. Fellows must receive their degree by the start of training or have received their degree no more than five years ago. Candidates must be a U.S. citizen or be eligible to work in the United States (after obtaining an appropriate visa). Desired skills: Strong candidates will have prior experience with programming and neuroimaging (broadly defined), including data collection and analysis, as well as conducting behavioral experiments. Interested candidates should email a cover letter briefly describing their research interests and qualifications, a curriculum vitae, as well as the names and contact information for three references to Anna Holubecki at: anna.holubecki(a)northwestern.edu Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women, racial and ethnic minorities, individuals with disabilities, and veterans are encouraged to apply. Hiring is contingent upon eligibility to work in the United States.

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Postdoctoral Opportunity at Albert Einstein College of Medicine (New York City)
by Benjamin Ely 16 Nov '20

16 Nov '20

External Email - Use Caution The Psychiatry Research Institute at Montefiore Einstein (PRIME), a division of the Department of Psychiatry and Behavioral Sciences at Albert Einstein College of Medicine, is seeking a highly motivated postdoctoral scholar in the field of human neuroimaging. The focus of this position will be on analyzing fMRI data as well as related MR and biological measures. Candidates should have (or be near completing) a PhD in neuroscience, psychology, cognitive science, radiology, engineering, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. Under the mentorship of Vilma Gabbay, MD, this postdoctoral scholar will be expected to advance both clinical and methodological knowledge through their postdoctoral training. Dr. Gabbay is the Director of Research at PRIME, a unique program in the greater New York metropolitan area dedicated exclusively to the study and treatment of adolescent mood and anxiety disorders, utilizing innovative neuroimaging and immunological methodologies. The neuroimaging program, led by Benjamin Ely, PhD, features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is dedicated to advancing the fields of magnetic resonance imaging and spectroscopy. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra, Philips Elition) with cutting-edge accelerated fMRI and edited MRS sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The primary responsibility for this postdoctoral fellow will be to analyze neuroimaging data from several ongoing and recently concluded research projects. Dr. Gabbay is fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. The initial employment period for this position is two years, with the possibility of extension. Salary will be competitive and commensurate with experience and the cost of living in New York City. Subsidized housing close to the Einstein campus in the Morris Park neighborhood of The Bronx is available. Please send a CV, statement of interest, and contact information for three references to Dr. Ely (benjamin dot ely at einsteinmed dot org) and to our Research Coordinator, Sherry Simkovic (sherry dot simkovic at einsteinmed dot org). Albert Einstein College of Medicine is an equal opportunity employer; all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner.

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Training in Advanced Statistics in Neuroimaging and Genetics, Feb 15 - 26, 2021 {Disarmed}
by ROBERT CARY WELSH 16 Nov '20

16 Nov '20

External Email - Use Caution Hi, We are pleased to announce the course, “Training in Advanced Statistics in Neuroimaging and Genetics”, to be held virtually in Salt Lake City, Utah, at the University of Utah: The University of Utah, with funding from the National Institute of Neurological Disorders and Stroke, is excited to announce this two-week course. The focus of this course is to learn advanced statistical methods applied to neuroimaging and genetics, within the context of biomarker discovery. This is not an introductory course, and will teach advanced topics, such as Bayesian methods in neuroimaging, network science in neuroimaging, statistical genetics, and multi-modal predictive modeling. Course attendees are expected to already have experience with aspects of neuroimaging analysis and/or genetics. An innovation to our course is the additional 6-month follow-up, where attendees have the opportunity to meet as a group with each lecturer for a 75-minute webinar-based workshop each month. This will allow attendees to interact with faculty well after the two-week period. Additionally, attendees will have access to a slack helpline for questions surrounding implementation of methods. For more information about the course, please visit: https://secure-web.cisco.com/1bFnaAETq3u6oXPqnEueq1P3xBb_4-RCBe0_TkGjv82tzq… Due to the COVID-19 pandemic, the 2021 course is being offered on-line live at a greatly reduced tuition rate of $250 (USD). There are a limited number of need-based “travel” awards (to cover tuition) available for eligible individuals. Because of the limited class size of 20 to 22, attendance is by application only. Applicants in general must be a US citizen or permanent resident, we do, however, have the ability to accommodate 1 to 3 individuals who do not meet the criteria. Applications deadline December 10th, 2020. Please visit: https://secure-web.cisco.com/1Ot11GbbN8kBPrSkhEezhtPckQLwEhCxGqjfO6pTYeKQQ6… for access to the application process. For more information, please email : advancedstatisticscourse (at) utah (dot) edu Follow us on twitter @neurostatscamp Cheers, Robert Welsh (robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu>), Course Director Anna Docherty (anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu>), Course Co-Director Department of Psychiatry University of Utah

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surf pial_lgi not created in version 7.1.0
by Kathy L. Pearson 16 Nov '20

16 Nov '20

External Email - Use Caution In freesurfer version 5.3.0, I can successfully run: recon-all -autorecon-all -mprage -s $subj -qcache -localGI recon-all -s $subj -qcache -measure pial_lgi However, the same commands with 7.1.0 give an error after this last of a number of generated statements and no surf/*pial_lgi output: mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find subjects/147608/surf/lh.pial_lgi Is a new command needed for version 7.1.0? Thanks, Kathy Pearson

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selxavg3-sess fails without useful error message
by Paul Soulos 16 Nov '20

16 Nov '20

External Email - Use Caution Hello, I am trying to run selxavg3-sess but it is failing without an error message so I am not sure how to proceed. selxavg3-sess works correctly for three of my subjects but fails on the fourth. I pasted a screenshot of the final lines below. In fast_selxavg3b, I can see the print message from line 168 <https://secure-web.cisco.com/19ZB_QI5mA5XMqz-HJfk4ohW11tW-tCeW-U3GVonV7PxHP…> but never see the print message from line 193 <https://secure-web.cisco.com/1L_etSbacHu5FU_fXDblxCh1IOvTaplFBDG9DlS-issWyI…> (which is the line I see next on the subjects that run correctly), so the code is failing out somewhere between these two lines. Do you have any guidance?I tried running selxavg3-sess with the `-debug` flag but it does not include any additional information that I could see. [image: image.png]

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Re: [Freesurfer] AAL Segmentation with Freesurfer {Disarmed}
by Douglas N. Greve 16 Nov '20

16 Nov '20

Please remember to post to the FS list ... That will not work because the AAL atlas is not in the same space. I think the AAL is in colin27 space, so download colin27, run recon-all, and then map the labels to the surface. On 11/15/2020 9:11 AM, Stephan Wunderlich wrote: > > External Email - Use Caution > > Thanks a lot for your reply. > > I was guessing that, but didn’t know how to tell the recon-all command > to use the AAL Atlas. And if I can just download the AAlv3 Atlas > (https://www.gin.cnrs.fr/en/tools/aal/ > <https://secure-web.cisco.com/1ha53fgZ8E-tHiie_WsIuzzloBAXNTlD4tdjnQFonGl8A9…>) > and put that folder into the freesurfer/average folder. > > Cheers,

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Re: [Freesurfer] Installing FreeSurfer on Windows 10 WSL Ubuntu System {Disarmed} {Disarmed}
by fsbuild 15 Nov '20

15 Nov '20

External Email - Use Caution Hello Mathew, It reads like you have installed WSL on Windows 10 and have Ubuntu running as the guest OS in WSL.  Then from the Ubuntu guest OS you are trying to download a freesurfer distribution using the Freesurfer download links. Using the links on this page, https://secure-web.cisco.com/1ihPjm6rvWaTegSRWzrfWft9z7YpRC0YNAkdS1L8dRJ9nN…, worked for me to download the freesurfer linux 7.1.1 tar.gz file using https://secure-web.cisco.com/1NA7i3FtvdZxLC1c5EAa9hLV7BdEZy_Wlwz8qXamY18sg0… You could also try downloading the archive into your Windows 10 home directory Downloads folder and then use the shared C drive mount point to copy the file from Windows into Ubuntu.  Or in an Ubuntu terminal window, you should be able to copy anything from under your Windows 10 home directory, e.g., named “matt", using this path in the Ubuntu terminal window, /mnt/C/Users/matt/Downloads After download in Windows, then in Ubuntu terminal window,$ cd $HOME$ cp /mnt/C/Users/matt/Downloads/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz  . ... then cd to wherever you want to expand the archive … $ cd <some directory>$ tar zxpf $HOME/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz - R. On Nov 15, 2020, at 22:14, Mathew Chu <mathew.chu(a)unsw.edu.au> wrote:        External Email - Use Caution        Dear Admin,I am having trouble downloading FreeSurfer onto my Ubuntu WSL. I have tried downloading various .tar.gz files for CentOS 7 from the FreeSurfer directory (e.g. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/) but the downloads do not seem to be starting at all.Any advice on this matter would be much appreciated,MathewPS. I've only recently confirmed my subscription to the mailing list, so I am resending this email request for help (the first email was rejected before I confirmed by subscription).From: Mathew ChuSent: Monday, 16 November 2020 1:22 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Installing FreeSurfer on Windows 10 WSL Ubuntu System Dear Admin,I am having trouble downloading FreeSurfer onto my Ubuntu WSL. I have tried downloading various .tar.gz files for CentOS 7 from the FreeSurfer directory (e.g. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/) but the downloads do not seem to be starting at all.Any advice on this matter would be much appreciated,Mathew_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Installing FreeSurfer on Windows 10 WSL Ubuntu System {Disarmed}
by Mathew Chu 15 Nov '20

15 Nov '20

External Email - Use Caution Dear Admin, I am having trouble downloading FreeSurfer onto my Ubuntu WSL. I have tried downloading various .tar.gz files for CentOS 7 from the FreeSurfer directory (e.g. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/<http://secure-web.cisco.com/1zOOiu4L7pd0OWg4_n-Yr3VnCp9vvJtYUpaGSEpy7j7oyVo…>) but the downloads do not seem to be starting at all. Any advice on this matter would be much appreciated, Mathew PS. I've only recently confirmed my subscription to the mailing list, so I am resending this email request for help (the first email was rejected before I confirmed by subscription). ________________________________ From: Mathew Chu Sent: Monday, 16 November 2020 1:22 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Installing FreeSurfer on Windows 10 WSL Ubuntu System Dear Admin, I am having trouble downloading FreeSurfer onto my Ubuntu WSL. I have tried downloading various .tar.gz files for CentOS 7 from the FreeSurfer directory (e.g. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/<http://secure-web.cisco.com/1zOOiu4L7pd0OWg4_n-Yr3VnCp9vvJtYUpaGSEpy7j7oyVo…>) but the downloads do not seem to be starting at all. Any advice on this matter would be much appreciated, Mathew

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