Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

T2/FLAIR for pial surface refinement
by Eva Hilland 15 Oct '14

15 Oct '14

Dear FreeSurfer experts I have been trying to do a test with T2/FLAIR for pial surface refinement, with T1 and FLAIR NiFti images for one subject, FS v5.3. As described in Release Notes i updated the recon-all script in /freesurfer/bin. I have also tried to do the -bbr-init-header . I used the forllowing commands: 1) recon-all -s [subject_name] -i T1.nii -all (wich ran succesfully.) 2) recon-all -autorecon3 -s [subject_name] -FLAIR FLAIR/flair.nii -FLAIRpial I have tried this many times the past week, on my MacBookPro and also on my lab computer running on Linux RedHat 6. But I get the "recon-all exited with ERRORS" every time, with the error message "Cannot allocate memory". I attached the recon-all.log. I also pasted the system information for my computer at the end of this e-mail. Is there anything I do wrong in the command? Does this process require a more powerful computer than you would need for regular recon-all? Thank you very much in advance! Best regards, Eva lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 6 On-line CPU(s) list: 0-5 Thread(s) per core: 1 Core(s) per socket: 6 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 44 Stepping: 2 CPU MHz: 2659.928 BogoMIPS: 5319.85 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 12288K NUMA node0 CPU(s): 0-5

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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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Freesurfer October 2014