Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

QAtools - tkmedit snapshots all black (X server issue?)
by Melanie Ganz 15 Oct '14

15 Oct '14

Hi, I am trying to use the QA tools and take some tkmedit snapshots. I can get everything to work fine in Boston, but when I run on our local Linux server what tkmedit shows looks correct, but the output gifs of tkmedit are all black with no content. The tksurfer images show and save fine. I am suspecting that it is an x server issue with how I log into our Linux cluster here, but has anyone had the same problem before? Cheers, Mel -- Melanie Ganz, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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Post-docs positions on MR-PET method development and application in Lyon (France)
by Marjorie Villien 15 Oct '14

15 Oct '14

Dear all, We are offering two post-doc positions on a newly installed MR-PET scanner in Lyon (France), at the CERMEP, for the LILI project (“Lyon Integrated Life Imaging: hybrid MRI-PET”). The application deadline is quite soon, before October the 28th, since the positions begin in January 2015. For details please see the attached PDFs. Best, Marjorie Villien -- -- Marjorie Villien, PhD Research Engineer CERMEP - imagerie du vivant 59 boulevard Pinel 69677 BRON Cedex - FRANCE Phone: (33) 04 72 68 86 34

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FIR analysis on regions of interest...
by Joseph Andreano 14 Oct '14

14 Oct '14

Hi All, I'm trying to extract signal from an ROI in an analysis that I specified as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce an output file that gives me a single value for each participant. What I'm trying to do is to get a value for each TR in the time window I specified so that I can generate a time course for that ROI. I know that this was possible with the older analysis tools in the older version of freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are just giving me a single (presumably averaged) value. Does anyone know how I can get a timecourse for my ROI? Thanks, Joe _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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cortical surface area measurement and vertex-wise analysis
by Emma Thompson 14 Oct '14

14 Oct '14

Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks!

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CentOs 7
by will brown 14 Oct '14

14 Oct '14

Hi, Is Freesurfer compatible with CentOs 7? Thanks, Will Brown

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Re: [Freesurfer] excluding labels
by Adam, Ruth 14 Oct '14

14 Oct '14

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Re: [Freesurfer] excluding labels
by Adam, Ruth 14 Oct '14

14 Oct '14

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Do not have a 'Recon edit'
by Smaragdi A. 14 Oct '14

14 Oct '14

Dear mailing list, I am not sure if the version of Freesurfer I have downloaded is old, or I have done something wrong, or I am just blind.. But I cannot find the 'recon edit' button in freeview (see attached screenshot). What amI not doing right? Many thanks, Areti

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POST DOCTORAL POSITION at The Neurofunctional Imaging Group in Bordeaux
by Fabrice Crivello 14 Oct '14

14 Oct '14

POST DOCTORAL POSITION in BORDEAUX The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research unit of the Bordeaux University (UMR 5296, dir. Bernard Mazoyer) and a core member of the TRAIL Laboratory of Excellence. The GIN is a multidisciplinary research unit gathering scientists with initial training in mathematics and instrumentation, cognitive neurosciences, signal processing and databasing. One objective of the current GIN research project is to develop new tools to characterize and describe the gray matter anatomical connectivity networks. Within this area we have a position for a 2 years Post Doc. Description of the position Recent work on brain connectivity modeling revealed that the topographic organization of this connectivity is not limited to large-scale anatomical pathways generally observable in diffusion MRI, thus reinforcing the interest of studies focusing on the characterization of cortical structural connectivity and its variability. Therefore, the estimation of relevant grey matter connectomes strongly relies on the choice of an ad'hoc cerebral parcellisation. We propose a post doc project to first implement a probabilistic cortical atlas derived from cortical parcellisations defined individually to optimally extract cortical thickness and volume of each individual. The second aim of the post doc project is to compute cortical structural connectivity to quantify the inter-individual variability of brain organization together with the effects of specific factors such as gender, manual preference, functional lateralization or cognitive skills. The strength of the present project is that it will benefits from the already acquired BIL&GIN database composed of 453 healthy volunteers balanced for gender and handedness. Hence, the first probabilistic cortical atlas will be operated over a large sample, the 453 participants having been previously pre-processed. Qualification and experience The qualified applicant should have a PhD in neuro-image analysis, cognitive neuroscience, computer science or related field and a background in neuroimage processing. Applicants should have experience with existing tools for analysis of neuroimaging data (SPM, FSL, Freesurfer.) and a relevant programming experience (MATLAB). For further information, please contact Dr. Fabrice Crivello (fabrice.crivello(a)u-bordeaux2.fr) Employment and payment are determined by Bordeaux University (2 400 € per month, net salary). Job location is in Bordeaux, France. Interested candidates should send their applications including CV with full publication list, the names and contact information and a summary of research interests to fabrice.crivello(a)u-bordeaux2.fr. Dr. Fabrice CRIVELLO Groupe d'Imagerie Neurofonctionnelle UMR 5296 - CNRS CEA Université Bordeaux Université de Bordeaux 146, rue Léo Saignat CS 61292 33076 Bordeaux Cedex Mob : +33 618 064 753 Tel : +33 547 304 402 Fax : +33 547 304 394 www.gin.cnrs.fr See my publications : https://www.researchgate.net/profile/Fabrice_Crivello

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Brainhack EDT - Boston Updates and Registration Details
by MCLAREN, Donald 13 Oct '14

13 Oct '14

*October 18th and 19th, Boston* *McGovern Institute for Brain Research @ MIT - * *http://whereis.mit.edu/?go=46* <http://whereis.mit.edu/?go=46> *3rd floor Atrium * *Doors will be locked, so we will have to let you in. If you are the door, please call 4-3544 or (617-324-3544) or send a chat message here: * *https://gitter.im/satra/brainhackEDT* <https://gitter.im/satra/brainhackEDT> *BRAINHACK EDT - BOSTON NEWS/UPDATES:* · Siemens is providing funds to help host Brainhack EDT - Boston. · The Brainhack EDT - Boston organizing committee is excited to announce that we will be providing lunch to attendees who register/confirm their attendance and food choices by 6PM on October 15th (see instructions below; http://goo.gl/tMfwa2) · The Brainhack EDT - Boston organizing committee is working on organizing a group dinner (attendee pays) on Saturday night in Cambridge. · Amazon will provide credits for cloud computing ($100 per person) · NeuroElectrics will be bringing a couple of their wireless EEG headsets for interested parties to hack on. Please check the column if you are interested. · All attendees must confirm their registration by following the registration instructions below. *REGISTRATION DETAILS:* With the generous support from Siemens, we will be providing lunch to attendees of Brainhack Boston. In order to receive lunch, you must confirm your registration (indicate YES/NO) and food choices by Noon on October 15th, 2014. Please click here to register: http://goo.gl/tMfwa2 When you are registering please provide us with your lunch choices along with whether or not you plan to attend the organized dinner on Saturday Night (attendees pay for their own dinner). If you do not provide us with your lunch choices, you will not get free lunch. In addition, please indicate whether you are interested in working with/on the Neuroelectrics headset. *PROJECT PROPOSALS:* We've heard rumors of several projects for Brainhack EDT - Boston. In order to spread the word of these projects, we request that you add your project(s) on the following page: http://goo.gl/fSMgc3 Project proposal introductions will be 1 minute. If you want to use a slide to introduce your project, please send the powerpoint slide to mclaren.donald-a(a)t-gmail.com *BRAINHACK EDT - BOSTON SCEHDULE:* *Saturday, October 18, 2014* 08:30 Attendee Arrival (with coffee) 09:00 Welcome reception 09:15 Ignite Talk with icebreaker 09:45 Project Pitch 10:00 Open Hacking 12:00 Onsite Lunch (Mexicali) 13:00 Crowd Annotation Projects (Dolphin Brain) 13:45 Unconference Session 15:00 Coffee Break 15:30 Open Hacking 18:30 Organized dinner (pay your own way) 20:30 Open Hacking *Sunday, October 19, 2014* 08:30 Attendee Arrival 09:00 Ignite Session II 09:30 Unconference Session 10:30 Open Hacking 12:30 Onsite Lunch (Mexicali) 13:30 Open Hacking 15:00 Coffee Break 15:30 Open Hacking 17:00 Project Summaries and Wrap-up 18:30 Adjournment 19:00 Optional Dinner or Open Hacking *The Boston Brainhack Committee* Donald G McLaren, MGH/HMS Satra Ghosh, MIT Matt Hutchison, Harvard University

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