Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

Postdoc in Microstructure Imaging analysis of Hearing Loss: From the ear to the brain network
by Tim B. Dyrby 27 Dec '19

27 Dec '19

External Email - Use Caution Hi FreeSurfer's, Here at DRCMR in Copenhagen we are searching for a postdoc - Are you interested in hearing loss and eager to find out which microstructural changes occur in the auditory system when hearing becomes impaired? Then you might be our new postdoc in the multidisciplinary project “Uncovering Hidden Hearing Loss” (UHeal). *You will be part of the research project UHeal* UHeal is a multidisciplinary project funded by the Novo Nordisk Foundation under the interdisciplinary synergy program and involves The Technical University of Denmark (DTU) (PI: Tosten Dau), Harvard Medical School (PI: Charles Liberman) and Danish Research Centre for Magnetic Resonance (DRCMR) (PI: Tim Dyrby and Hartwig Siebner). Together we will design imaging techniques and auditory methods to detect and diagnose a recently described damages to the auditory nerve caused by exposure to loud sounds. Such damage can cause a ‘hidden hearing loss’ that a large part of the world population may have without knowing it. You can read more about the project at http://www.drcmr.dk/uhealand http://www.hea.healthtech.dtu.dk/research/Uncovering-Hidden-Hearing-Loss *Your contribution to the project * You will be working with microstructure imaging analyses and be responsible foradvancing structural magnetic resonance imaging (MRI) of the human auditory system UHEAL. It will be your responsibility to establish the data analyze setup of microstructural imaging data to map the hearing system, from the ear to the brain network in health and disease. You will also be involved in establishing the imaging protocols on a 3T Prisma human MRI scanner to ensure optimal microstructure imaging contrast for hearing loss. The scanning protocols can include a combinations of myelin mapping using quantitative MRI, multi-dimensional diffusion MRI and DTI for insights into microanatomy, or simply T1W or T2W MRI. You will be part of the interdisciplinary UHeal team exploring the structural functional relationship in hidden hearing loss and together with postdocs and researchers from the other sites you will compare the microstructure imaging analysis with their functional measures and novel hearing loss tests on the same subject group. * The ideal candidate* Should be a motivated international minded team player with: -A PhD degree or corresponding qualification in engineering, physics or computer science. -A strong documented background in diffusion MRI and data analysis of human data. -Proficiency regarding using human MRI scanners, preferably Siemens. -Excellent written and oral communication skills in English *Your tasks* * To advance the field through your own research * To work directly with a dedicated and inspiring cross disciplinary team and international collaborators. * To establish the data analysis for mapping microstructural changes in hearing loss in human subjects. * To be involved in establishing the imaging protocol and data collection on subjects * To be engaged in supervision of BSc, MSc and PhD students, knowledge dissemination and publishing in international, recognized scientific journals. ** *You will be working at DRCMR* You will be part of the Microstructure and Plasticity <http://www.drcmr.dk/map>(MaP) group headed by Tim Dyrby (www.drcmr.dk/map <http://drcmr.dk/map>) at The Danish Research Centre for Magnetic Resonance (DRCMR, www.drcmr.dk <http://www.drcmr.dk>). MaP is a dedicated cross-disciplinary and translational research team with thevision to improve the future non-invasive imaging technologies for better patient diagnosis. Your part of the UHeal project will be carried out at DRCMR but you will be collaborating intensively with the other project partners at DTU and Harvard. The project will be carried out at (DRCMR) which is a leading research center for biomedical MRI in Europe (www.drcmr.dk).Our mission is to triangulate MR physics and basic physiology from preclinical to clinical research. Approximately 75 researchers from a diverse range of disciplines are currently pursuing basic and clinically applied MR research and its validation with a focus on structural, functional, and metabolic MRI of the human brain and its disorders. The DRCMR is embedded in the Center for Functional and Diagnostic Imaging and Research, a large diagnostic imaging department including all biomedical imaging modalitiesat the *Copenhagen University Hospital Hvidovre*. DRCMR has a state-of-the-art MR-research infrastructure enabling translational research, which includes a pre-clinical 7T MR scanner, six whole-body MR scanners (one 7T, three 3T and two 1.5T scanners) and a High-Performance Computer cluster for neuroimaging. The DRCMR has pre-clinical labs, a neuropsychology laboratory, an EEG laboratory, and two laboratories for non-invasive brain stimulation. *Application deadline: 6^th January*2020*** **Starting date: *is expected to be in March 2020 or as soon as possible Interviews will take place in the first half of January Please read mere here: http://drcmr.dk/vacancies/item/1030-postdoc-in-microstructure-imaging-analy… Happy New Year, Tim -- Tim B. Dyrby Associate Professor Microstructure and Plasticity (MaP) Group Danish Research Centre for Magnetic Resonance (DRCMR), section 714 Center for Functional and Diagnostic Imaging and Research Copenhagen University Hospital Hvidovre Kettegård Allé 30 2650 Hvidovre Denmark Office phone: +45 38626542 Mobile:+45 40790282 web:www.drcmr.dk/map andwww.drcmr.dk & Image Analysis and Computer Graphics section Department of Applied Mathematics and Computer Science Technical University of Denmark Richard Petersens Plads, Building 324 2800 Kongens Lyngby Denmark Office Phone: +45 45253424

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Save output as attach file
by Nader Razmara 24 Dec '19

24 Dec '19

External Email - Use Caution Dear I want to save output of freeview as attach file. Which is a segmentation after thick colourmap ad lookptable and thick outline. Best regards

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BrainStem & HippoAmyg segmentation
by Meena M. Makary 23 Dec '19

23 Dec '19

External Email - Use Caution Hi, I am using Freesurfer stable6_0_0 (/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin) and I used it for all my subjects, so far. Now I would like to do BrainStem and HippocampalSubfieldsAndNucleiOfAmygdala segmentation which needs me to switch to dev versions. Should I switch to the dev version for getting this segmentations only and switch back Version 6 for future reconall or is it okay to switch to the dev version for good? In other words is there any differences in the reconall between the two versions? Thank you! Meena -- — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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Re: [Freesurfer] Qdec support {Disarmed}
by fsbuild 23 Dec '19

23 Dec '19

External Email - Use Caution Hello Leona, What is the error that you are seeing? Qdec is a 32 bit program (*not* 64 bit), so even Mac OS 10.14 (Mojave) may put up a warning that it is not optimized and needs to be re-compiled, but it should still run.  It will not however run if you upgrade to Catalina (Mac OS 10.15).  Mac OS 10.14 is the last version of the OS that will run any 32 bit applications. - R. On Dec 23, 2019, at 08:34, Leona.Salewski(a)med.uni-duesseldorf.de wrote:        External Email - Use Caution        Dear experts,i was trying to run Qdec on macOS Mojave, in the past it always worked well.But now I am not able to generate stats data any more, an error message pops up every time I try running it. Is there a general problem running Qdec or is it just a problem of mine? Kind regards L. SalewskiUniklinikum DüsseldorfGermany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Qdec support
by Leona.Salewski＠med.uni-duesseldorf.de 23 Dec '19

23 Dec '19

External Email - Use Caution Dear experts, i was trying to run Qdec on macOS Mojave, in the past it always worked well. But now I am not able to generate stats data any more, an error message pops up every time I try running it. Is there a general problem running Qdec or is it just a problem of mine? Kind regards L. Salewski Uniklinikum Düsseldorf Germany

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postdoc positions in Weill Cornell Radiology in NYC
by Tracy A. Butler 21 Dec '19

21 Dec '19

External Email - Use Caution Multiple Postdoctoral Research Scientist Positions Position Summary The newly formed Brain Health Imaging Institute (BHII) in the Department of Radiology of Weill Cornell Medicine is seeking highly qualified applicants for multiple postdoctoral research scientist positions for duration of up to three years. The BHII, a multidisciplinary research group headed by Dr. Mony de Leon, designs and implements cutting edge MRI and PET neuroimaging methods to study brain function in normal aging, and in disease states including Alzheimer’s Disease and Traumatic Brain Injury. In addition to neuroimaging, the BHII has expertise in fluid (blood and CSF) biomarkers, detailed cognitive and neurologic assessment and neuropathological examination. Postdoctoral researchers will have access to state of the art neuroimaging and other equipment including an on-site cyclotron and radiochemistry facilities and multiple MR (3T and 7T), PET/CT and PET/MR scanners. Weill Cornell Medical College, located in the upper east side of New York City, has a vibrant biomedical research community and strong ties to the main Cornell campus in Ithaca and the Tech campus on Roosevelt Island. Responsibilities: * Under the direct supervision of Dr. Tracy Butler, develop and apply cutting-edge research methods such as MRI, PET (to study amyloid, tau, brain clearance, inflammation and/or other biological processes) and/or complementary techniques such as statistical interrogation of existing datasets, EEG, neuropathology or biospecimen wet-lab assays to understanding brain functioning in healthy subjects and in subjects suffering from a variety of disease states both common (Alzheimer’s Disease, Traumatic Brain Injury) and under-studied (victims of domestic violence, autoimmune encephalopathy.) * Disseminate research results through publications in high-impact journals and presentations at top international conferences * Support and mentor research of other fellows and students with medical or engineering background Qualifications: * MD or PhD in Neuroscience, Neuropsychology, Electrical/Biomedical Engineering, Computer Science, Applied Mathematics, Statistics or related field * Significant track record of research and publications in top scientific conferences and journals * Effective communication skills, both written and verbal * Track record of effectively working both independently and as part of a multidisciplinary team Highly Desired Knowledge in one or more of the following: * Brain anatomy and physiology * Neuroimaging, especially of functional/structural MRI and PET * PET kinetic modeling * Familiarity with common neuroimage processing tools, e.g. FreeSurfer, FSL, AFNI, SPM, PMOD. * Statistical or mathematical models of biological systems To apply: Please send a one-page statement of career goals and research interests and full CV to tab2006(a)med.cornell.edu with subject title: Application for postdoctoral research scientist position. Weill Cornell Medicine: Founded in 1898, and affiliated with what is now New York Presbyterian Hospital (NYPH) since 1927, Weill Cornell Medicine (WCM) is among the top-ranked clinical and medical research centers in the country. In addition to offering degrees in medicine, WCM also has PhD programs in biomedical research and education at the Weill Cornell Graduate School of Medical Sciences, and with neighboring Sloan-Kettering Institute and The Rockefeller University, has established a joint MD-PhD program for students to intensify their pursuit of Weill Cornell's triple mission of education, research, and patient care. WCM is divided into 24 basic science and patient care departments that focus on the sciences underlying clinical medicine and/or encompass the study,treatment, and prevention of human diseases. The basic science and clinical departments are located in buildings that straddle York Ave. between 68th and 72nd streets on Manhattan’s Upper East Side. Weill Cornell Medical College has 1781 full time faculty (3582 total faculty) distributed across 8 basic science and 15 clinical departments. WCM maintains major affiliations with Memorial Sloan-Kettering Cancer Center, The Rockefeller University, the Hospital for Special Surgery, as well as with the metropolitan-area institutions that constitute NYP Healthcare Network. Weill Cornell Medicine is a comprehensive academic medical center that's committed to excellence in patient care, scientific discovery, and the education of future physicians in New York City and around the world. Our doctors and scientists-faculty from Weill Cornell Medical College, Weill Cornell Graduate School of Medical Sciences, and the Weill Cornell Physician Organization-are engaged in world-class clinical care and cutting-edge research that connect patients to the latest treatment innovations and prevention strategies. Located in the heart of the Upper East Side's scientific corridor, Weill Cornell Medicine's powerful network of collaborators extends to its parent university Cornell University; to Qatar, where an international campus offers a U.S. medical degree; and to programs in Tanzania, Haiti, Brazil, Austria and Turkey. Our medical practices serve communities throughout New York City, and our faculty provide comprehensive care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center, NewYork-Presbyterian/Lower Manhattan Hospital, and NewYork-Presbyterian/Queens. At Weill Cornell Medicine, we work together to treat each individual, not just their conditions or illnesses, as we strive to deliver the finest possible care for our patients - the center of everything we do Weill Cornell Medicine is an Equal Employment Opportunity Employer. Weill Cornell Medicine provides equal employment opportunities to all qualified applicants without regard to race, sex, sexual orientation, gender identity, national origin, color, age, religion, protected veteran or disability status, or genetic information.

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Error running "Test your FreeSurfer Installation"
by Rafael Espericueta 21 Dec '19

21 Dec '19

External Email - Use Caution I was trying to run the command: recon-all -s bert -all It ran for hours, but finally output the following: writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 18.04.3 3) recon-all.log: see attached

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Re: [Freesurfer] Thickness problem
by Gwang-Won Kim 20 Dec '19

20 Dec '19

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Manual segmentation to volume
by Benjamin Ineichen 20 Dec '19

20 Dec '19

External Email - Use Caution Dear Freesurfer experts, I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map. In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried: mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz the example_orig.mgz would correspond to the original T1 which I used to do the segmentation. But this gives me the error message: ERROR: could not determine type of talairach.xfm ERROR: reading talairach.xfm header Where is the problem? Many thanks! /Ben

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Creating a label from overlapping cluster results
by cody samth 20 Dec '19

20 Dec '19

External Email - Use Caution Hi, I was wondering if there is any automated command/method to create a new label that consists of the overlap of two labels? I've run two whole brain analyses with different predictors and have regions where the clusters from each analysis overlap. I'm interested in creating a label for visualization purposes and to extract cortical data in these regions of overlap. Thanks, Cody

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Freesurfer December 2019