Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Research Assistant Positions in ECoG Lab in New York
by steph 16 Jan '18

16 Jan '18

Dear all, The ECoG Laboratory for Human Brain Mapping at the Feinstein Institute for Medical Research – Hofstra Northwell School of Medicine is looking for two research assistants. The successful candidates will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as electrocorticography (ECoG), MRI, fMRI, DTI, and direct electrical brain stimulation. The start date is as soon as possible. The responsibilities of both research assistants include assisting with the collection and analysis of the aforementioned data, managing lab equipment, and helping to present lab findings at conferences and in journals. One position will further focus on project management and administration, working with a research coordinator on IRB matters, and assistance with preparing progress reports and grant applications. The second position is more computationally focused and will require more in-depth analysis of neural and behavioral data, database management, and the development of analysis scripts (depending on proficiency with coding and signal processing). Both RAs will have their own scientific projects with dedicated time to work on them. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. These unique positions will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -For the second RA position: Experience with at least one programming language (MATLAB, R, or Python) and statistical analyses -1 year commitment Desirable: -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -2 year commitment preferred For more information about the position please send your CV along with your questions to Drs. Stephan Bickel (sbickel(a)northwell.edu <mailto:sbickel@northwell.edu>) and Ashesh Mehta (amehta.northwell.edu <http://amehta.northwell.edu/>). We are looking forward to hearing from you!

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PhD and postdoctoral positions - Investigating sensory aspects of human communication
by Katharina von Kriegstein 16 Jan '18

16 Jan '18

Several researcher positions (Postdocs and PhD students) are available at the Human Communication Research Group, led by Katharina von Kriegstein. The group is currently based at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig (MPI CBS; http://www.cbs.mpg.de/independent-research-groups/human-communication ) and will transfer to the Psychology Faculty of the TU Dresden in 2018. The positions are funded by the ERC consolidator grant SENSOCOM. The aim of the SENSOCOM project is to investigate the role of auditory and visual subcortical sensory structures in analysing human communication signals and to specify how their dysfunction contributes to human communication disorders such as developmental dyslexia and autism spectrum disorders. For examples of our work on these topics see von Kriegstein et al., 2008 Current Biology, Diaz et al., 2012 PNAS; Müller-Axt et al., 2017 Current Biology. The projects include experiments using cognitive neuroscience methods to understand the basic mechanisms of cortico-subcortical interactions as well as development of training programmes that are aimed at creating behavioural intervention programmes for communication deficits (for a brief description see http://cordis.europa.eu/project/rcn/199655_en.html ). The positions will be based at the TU Dresden. Research will be performed at the Neuroimaging Centre at the TU Dresden ( http://www.nic-tud.de ) and MPI CBS in Leipzig. The centres offer cutting-edge infrastructure with 3-Tesla MRI, 7-Tesla MRI, a Connectom scanner, MRI compatible eye-tracking, several EEG systems, 306-channel MEG, neurostimulation units including neuronavigaton, TMS and tDCS devices. Besides an excellent infrastructure, the centres offer an international and friendly environment with researchers from diverse backgrounds. All experimental facilities are supported by experienced physics and IT staff. For analyses with high computational demands, there is access to high-performance computing clusters. Candidates should have a strong interest in perceptual aspects of human communication and experience with experimental methods of cognitive neuroscience, such as psychophysics, functional or structural MRI, TMS, diffusion-weighted imaging, brainstem recordings or EEG/MEG. Experience with clinical populations (e.g. developmental dyslexia) would be an asset but is not essential. PhD student candidates must have a Master’s degree (or equivalent) in neuroscience, clinical linguistics, psychology, cognitive science, biology, or a related field. Postdoc candidates must have a PhD in similar fields and should be able to demonstrate a consistently outstanding academic record, including publications. The position starting date is flexible. Initially for two (postdocs) or three (PhD) years, the positions offer the possibility of an extension. Remuneration depends on experience and is based on regulations of the Max Planck Society payscale. MPI CBS is an equal opportunities employer, committed to the advancement of individuals without regard to ethnicity, religion, gender, or disability. PhD students will have the opportunity to participate in the TU Dresden graduate academy (https://tu-dresden.de/ga?set_language=en) TU Dresden is one of eleven German Universities of Excellence and offers an interdisciplinary scientific environment. To apply, please submit a CV, contact information of two references, a brief personal statement describing your qualifications and future research interests, copies of up to two of your publications. Please submit your application via our online system at http://www.cbs.mpg.de/vacancies (using subject heading “ERC 01/18”). The deadline for application submission is 15st February 2018. Contact for informal enquiries regarding the post: Prof. Dr. Katharina von Kriegstein (katharina.von_kriegstein(a)tu-dresden.de) --- Prof. Dr. Katharina von Kriegstein Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Technische Universität Dresden Bamberger Str. 7, 01187 Dresden, Germany Phone +49 (0) 341-9940-2476 http://www.cbs.mpg.de/independent-research-groups/human-communication https://twitter.com/kvonkriegstein

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Re: [Freesurfer] Amygdala segmentation runtime error
by Iglesias Gonzalez, Eugenio 15 Jan '18

15 Jan '18

Hi Emily, When did you download the dev version? Was it very recently? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Emily K Clarke <ekc23(a)duke.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 11 January 2018 at 20:57 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Amygdala segmentation runtime error Hi Freesurfer developers, I’m attempting to run the new amygdala segmentation command (segmentHA_T1.sh) using the developer version of Freesurfer 6.0. However, when I run my script I receive the following error — error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory I checked with our cluster administrator, and we do have the Matlab R2012 runtime installed. Does anyone have any insight into what could be causing this error? I’ve attached my full output as well as my script in case that’s any help! Thanks, Emily K. Clarke Duke University

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Join us for HCP Course 2018 in Oxford, UK June 25-29!
by Jennifer Elam 15 Jan '18

15 Jan '18

We are pleased to announce the *2018 HCP Course: "Exploring the Human Connectome" <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…>*, to be held *June 25 – 29, 2018* at the Blavatnik School of Government <https://www.bsg.ox.ac.uk/partner/contact-us>, at the University of Oxford <http://www.ox.ac.uk/>, in Oxford, UK. This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data using methods and tools developed by the WU-Minn-Oxford Human Connectome Project (HCP) consortium. FreeSurfer is a major part of the HCP structural processing pipeline, has been critical to the processing of the HCP Young Adult project's over 1100 released high quality imaging datasets, and continues to be used in the processing of forthcoming Lifespan HCP data. The HCP course is designed for investigators interested in: - using HCP-style data distributed by the Connectome Coordinating Facility (CCF) from the young adult (original) HCP and forthcoming projects - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench <https://www.humanconnectome.org/software/connectome-workbench.html> tools and sharing data using the BALSA <https://balsa.wustl.edu/> imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - positioning yourself to capitalize on HCP-style data forthcoming from large-scale projects currently collecting data (e.g., Lifespan HCP development and aging and Connectomes Related to Human Disease projects) Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data. Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. The course is open to students, postdocs, faculty, and industry participants. The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including some familiarity with FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki> and Freesurfer <https://surfer.nmr.mgh.harvard.edu/> software. For more info and to register visit the <https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto…>HCP Course 2018 website <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…>. New this year is the opportunity to add 6 nights of bed and breakfast accommodation (Sun June 24 - Fri June 29) at nearby Worcester College to your registration at a group, taxes included rate. If you have any questions, please contact us at: hcpcourse@humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Organizers -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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POST-DOCTORAL RESEARCH ASSOCIATE IN CLINICAL NEUROSCIENCE OHIO STATE UNIVERSITY
by Herring, Elizabeth J. 15 Jan '18

15 Jan '18

<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html><http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> <http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html><http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> POST-DOCTORAL RESEARCH ASSOCIATE IN CLINICAL NEUROSCIENCE <http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html>OHIO STATE UNIVERSITY <http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> <http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> The Clinical Neuroscience Lab<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html>, in the Department of Psychology, within the College of Arts and Sciences, seeks a Post-Doctoral Researcher to join our team. The College of Arts and Sciences is the largest college and the academic heart of the university. The College hosts 81 majors. With 38 departments, 20+ world-class research centers, and more than 2,000 faculty and staff members, students have the unique opportunity to study with the best artists, scholars, and scientists in their field. The College values diversity and offers a supportive, open, and inclusive community. The Clinical Neuroscience Lab is directed by Dr. Ruchika Prakash and the laboratory is funded by the National Institute of Health and the National Multiple Sclerosis Society. The postdoctoral researcher will be involved in research examining the effects of various lifestyle interventions, like mindfulness meditation and exercise training, on cognitive and affective regulation. Using theoretically motivated behavioral and neural measures, our goal is to rigorously examine the effect of engaging in such interventions for attentional control, emotion regulation, and everyday cognition in older adults, examining the effects of various lifestyle interventions, like mindfulness meditation and exercise training, on cognitive and affective regulation. Successful candidates must have earned a doctorate in Psychology (preferably clinical, with an emphasis on neuropsychology or health psychology) and have strong clinical skills to collaborate on a five-year, NIH-funded randomized controlled trial on mindfulness meditation. Experience with fMRI and/or EEG is desirable but not necessary. Additionally, the successful candidate should demonstrate strong communication skills through peer-reviewed publications and national presentations. Commitment to graduate and undergraduate training plus an interest in pursuing grants from federal agencies and private foundations is expected. Position available for one year with additional years dependent on satisfactory performance and availability of funding. Apply online at: https://www.jobsatosu.com, under job listing #435091 and submit a CV, a brief statement of research interests, the expected date of availability, and the names and contact of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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Longitudinal Pipeline
by Aaron Tanenbaum 15 Jan '18

15 Jan '18

I am interested in knowing what type of alignment goes into the last stage of the longitudinal pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find the warp?

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regional gray matter volumes and corticl thicknesses analysis in children
by Liu Y 15 Jan '18

15 Jan '18

Dear Experts, Is there an acurate way to anayze the longitudianl changes in regional gray matter volumes and corticl thicknesses in children (several months to 8 years). How accurate are freesurfer of fsl-FIRST? Best regards, Yawu

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White/pial surface failure
by Trevor K Day 12 Jan '18

12 Jan '18

Hello, We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our subjects. Two images from recon_checker are attached. I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there no obvious indication of any error. I’m not sure what to search because I don’t have an error message. Recon-all.log is attached. The brainmask is fine. Not perfect, but certainly not poor enough to cause this. The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in the frontal lobe, but nothing that freesurfer hasn’t handled before. Others have suggested that this seems to extreme to fix with control points, are the other approaches to take? The command used was: /usr/local/freesurfer/stable6_0/bin/recon-all \ -all -s 170661.s1 -hires -cw256 -qcache \ -i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \ -expert /mnt/panuc/udallp2/lib/expert.opts (Again, T1_256.nii.gz looks totally fine.) The contents of expert.opts are mris_inflate -n 30 * Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 * Platform: Debian GNU/Linux 8.9 (jessie) * Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64 GNU/Linux Where can I start to debug and fix this? Thanks, Trevor Day

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no skullstrip
by Dijkshoorn, A.B.C. (Aicha) 12 Jan '18

12 Jan '18

Dear free surfer developers, Because I work with neonatal scans the skullstrip phase cannot be applied correctly (it removes too much skull). To avoid this problem I added the -noskullstrip option. However, I do still need the brain mask output of this phase. How can I work around this? Kind regards, Aicha

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Re: [Freesurfer] making masks with subfields etc
by Iglesias Gonzalez, Eugenio 12 Jan '18

12 Jan '18

Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon(a)rcsi.ie> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 12 January 2018 at 13:07 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] making masks with subfields etc Hi FS experts, I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography. 1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to? 2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps? 3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths <input imgae> -thr LUT number of the subcorical structure -uthr lut number again <output filename> first and then regsiter them to the rawavg.mzg? Thanks for any guidance which is always greatly appreciated. Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D38BB0.B4949E20] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.ie<http://www.rcsi.ie/> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE

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Freesurfer January 2018