Freesurfer November 2020

freesurfer@nmr.mgh.harvard.edu

107 participants
149 discussions

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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Freeview - hide coordinate labels in scripts for screenshots {Disarmed}
by Chris Adamson 15 Nov '20

15 Nov '20

External Email - Use Caution Freesurfer people, Is there an option for freeview scripts to hide the coordinate labels in 2D view? They are appearing in screenshots and I want to get rid of them. Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> http://secure-web.cisco.com/17gCAgLCjVbT_69xPLIjWlmKUVdiSJ_q8C1cZ6k7FHD__nT…<http://secure-web.cisco.com/1nfoUXGRwD60vZ-KHs-6omqwHN9tA3jMSMlcVDfpxshu4Wq…> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Problem with volumes of hypothalamic segmentation
by Iglesias Gonzalez, Juan E. 13 Nov '20

13 Nov '20

Dear all, We have found a problem with the volumes of the hypothalamic units in our recently released volume, which we are working to fix ASAP. So, just to be clear the segmentations are fine, but the estimations of the volumes of the nuclei (i.e., the CSV files) are not. Apologies for any inconvenience this may have caused. We’ll let you know when the problem has been fixed (hopefully a matter of days). Kind regards, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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Sulc maps
by Reza Rajimehr 13 Nov '20

13 Nov '20

External Email - Use Caution Hi, In the .sulc files, the range of sulcal depth values are very different (about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is there just a simple scaling factor here, or the procedure for calculating sulcal depth has been changed? Thanks, Reza

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Freesurfer November 2020