[Freesurfer] Research engineer in Neuroimaging wanted
Dear Freesurfer list, the 'Institut de Neuroscience de la Timone <http://int.univ-amu.fr>' (INT), Marseille, France, is looking for a research engineer for a duration of one year. The candidate will bring a scientific support to MR neuroimaging research. If satisfactory, the contract will lead to a permanent position as an Aix-Marseille University research engineer at INT. Do not hesitate to pass this annoucement to anybody interested. Full details are available following this link <https://amubox.univ-amu.fr:443/index.php/s/pUDtyMjJEI2VoxP>. contact: olivier.cou...@univ-amu.fr -- Olivier Coulon, CNRS Research Director Aix-Marseille University, Institut de Neurosciences de la Timone Faculté de Médecine, 27 Bd Jean Moulin 13005 Marseille - France MeCA Research Group http://www.meca-brain.org https://sites.google.com/site/oliviercoulon olivier.cou...@univ-amu.fr <mailto:olivier.cou...@univ-amu.fr> Tel: +33 (0)4 91 32 40 59 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Mindboggle official software release and publication!
Thanks to Docker, you can run it on a mac, it's all explained on the Mindboggle website. Olivier Shane Schofield a écrit : Hello, Thanks. Seems very interesting! Is there any way to run this on Mac? Cheers -- Shane Schofield ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: concerting surface format
Hello Trisanna, as pointed out by Matt as I started to write this email, the solution is in the Gifti format. If you install brainvisa, it provides tools to convert from .mesh to .gii. You can then read these in FreeSurfer or convert them using mri_convert. You can write to me privately if you want to have more details about how to perform the conversion using Brainvisa. Best, Olivier Bruce Fischl <mailto:fis...@nmr.mgh.harvard.edu> 15 juin 2016 16:39 Hi Trisanna, perhaps check with the BrainVisa people? We don't know the specs of that format. Maybe you could read it into matlab, then write it out in our format with write_surf.m? cheers Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Trisanna Sprung-Much <mailto:trisanna.sprung-m...@mail.mcgill.ca> 15 juin 2016 16:33 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Trisanna Sprung-Much <mailto:trisanna.sprung-m...@mail.mcgill.ca> 14 juin 2016 22:12 Hi there is there a way to convert .mesh (BrainVisa) to the Freesurfer surface format? mri_convert doesn't seem to do it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Olivier Coulon, Aix-Marseille University, LSIS Laboratory CNRS Director of Research, olivier.cou...@univ-amu.fr <mailto:olivier.cou...@univ-amu.fr> http://olivier.meca-brain.org MeCA Research Group http://www.meca-brain.org Institut des Neurosciences de La Timone Faculté de Médecine, 27 Bd Jean Moulin, 13005 - Marseille, France Tél: +33 (0)4 91 32 40 59 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Postdoctoral position available
Dear list members, please find below a link to a postdoc position annoucement that might be of interest, in the field of cortical morphometry for developmental studies and autism. http://www.meca-brain.org/2016/05/31/we-are-looking-for-a-post-doc/ O. Coulon -- Olivier Coulon, Aix-Marseille University, LSIS Laboratory CNRS Director of Research, olivier.cou...@univ-amu.fr <mailto:olivier.cou...@univ-amu.fr> http://olivier.meca-brain.org MeCA Research Group http://www.meca-brain.org Institut des Neurosciences de La Timone Faculté de Médecine, 27 Bd Jean Moulin, 13005 - Marseille, France Tél: +33 (0)4 91 32 40 59 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Two positions (post-doc and software engineer) in Marseille, France
Title: signatureMail2011 Dear all, we have two positions opening in Marseille, France, for the study and modelling of brain development. Descriptions can be found at the following URLs: https://dl.dropboxusercontent.com/u/3372764/EngineerPosition_lefevreMarseille.pdf https://dl.dropboxusercontent.com/u/3372764/PostDocPosition_lefevreMarseille2.pdf If interested, pease contact Dr Julien Lefvre at: julien.lefe...@univ-amu.fr Olivier -- Olivier Coulon,CNRS research Fellow, olivier.cou...@univ-amu.fr Tel: +33491828527fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr LSIS Laboratory, IM TeamESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE http://www.lsis.org/brainmorph ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Research Assistant position
Title: signatureMail2011 Dear All, please find below an announcement for a research assistant position. --- Neuroimaging Research Engineer - Centre IRMf de La Timone, Marseille, France Recruitment date: May 2013 Application closing date: May 15th, 2013 Contract duration: 30 months Salary: 19.000 24.000 Euros / year, depending on experience Context The La Timone fMRI Centre (http://irmfmrs.free.fr/) of the Institut des Neurosciences de La Timone (http://www.int.univ-amu.fr/) in Marseille provides neuroscientists, medical researchers, and psychologists from the Aix - Marseilles area and beyond with Magnetic Resonance Imaging (MRI) services. The Centre operates a 3 Tesla MR system fully dedicated to neuroscience and psychology research in human and non-human primates and equipped with high-end stimulation and recording systems. The Centre, affiliated to CNRS and Aix-Marseille University, is involved in clinical, fundamental and methodological research and technical development through collaboration with local, national and international research groups and with a strong involvement in training and teaching. Mission The post holder will have for mission to assist the user community with basic and advanced analysis of cerebral MRI data (functional and structural). Specifically, tasks include: - Advise and help users with standard analysis of brain MR data - Help users with advanced analyses such as functional connectivity, diffusion tensor imaging, tractography, multivariate analysis, morphometry, ... - Develop and optimize software pipelines - Assist with the design and set-up of new studies - Contribute to education and training of the users Profile of the candidate Background in neuroimaging essential Experience with brain image analysis packages (e.g., SPM, Freesurfer, BrainVISA or FSL) Experience with development of brain image analysis methods or/and their application to neuroimaging studies desirable Good knowledge of statistical methods and tools Expertise with one or several programming languages (Matlab, Python, C/C++) Autonomy, initiative, ability to work at the interface between multidisciplinary teams Information requests and applications should be addressed to jean-luc.an...@univ-amu.fr, patricia.romaigu...@univ-amu.fr, and pascal.be...@univ-amu.fr -- Olivier Coulon, CNRS research Fellow, Head of the ImagesModels team olivier.cou...@univ-amu.fr Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr LSIS Laboratory, IM Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE http://www.lsis.org/brainmorph ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] PhD position available at Aix-Marseille University
Title: signatureMail2011 Dear all, please find below a PhD position offer: PhD position: shape analysis applied to neuroimaging. The LATP (http://latp.univ-mrs.fr) and LSIS (http://www.lsis.org) labs, Aix-Marseille University, France, are seeking a candidate for a PhD in the field of shape analysis applied to neuroimaging. Candidate: We are looking for an excellent Ph.D. candidate with a good background in applied mathematics and/or image analysis as well as an interest for neuroimaging. A minimum level of programming skills is required (Matlab, Python, C++). The applicant must have completed Master studies in applied mathematics, computer science, or image analysis prior to starting the program. Excellent academic results during the Master studies are required. The candidate is expected to start in September-October 2013. Context: The project is part of a collaboration between the two laboratories which will provide a co-supervision of the PhD student. The LATP lab is a fundamental and applied mathematics lab based in Marseille that includes a team specialised in probabilities, statistics, and signal processing. The LSIS lab is a computer science and information technology lab that includes a team specialised in image analysis with many years of experience in neuroimaging. Salary: roughly 1600/month (before tax but including health insurance, social security and fees) Project: The project is dedicated to the study of shape representations and distances between shapes. In particular, shape representations using directly the surface of the shapes, such as currents, and those using scalar maps describing the geometry of the shapes, such as Laplacian eigenfunctions, curvelets or shearlets, need to be compared. Their ability to capture global, local, or multiscale directional information is of particular interest. The goal is to produce methods that can be used to perform cortical morphometrics and characterize cortical folding patterns. Both labs can provide a solid theoretical environment and access to large databases of neuroimaging data. Information and applications: Please send your application including your CV with a letter of motivation, and a list of courses you followed with grades and evaluations to frederic.rich...@univ-amu.fr julien.lefe...@univ-amu.fr olivier.cou...@univ-amu.fr -- Olivier Coulon, CNRS research Fellow, Head of the ImagesModels team olivier.cou...@univ-amu.fr Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr LSIS Laboratory, IM Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE http://www.lsis.org/brainmorph ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] convert mnc-analyze-mgz
Thanks for the answer. The problem comes from my original analyze file, not from the conversion or recon_all. Olivier Doug Greve a écrit : It does not require neurological/radiological. It only requres that the geometry in the input file be accurate. Is it? You can test it by viewing it in tkmedit. doug Olivier Coulon wrote: Doug Greve a écrit : How do you know it is left-right swapped? What tool are you using to visualize it? Do you have a fiducial? Hello, the surface reconstruction (visualised with scuba) gave a left hemisphere that should be the right one (I am using icbm data that have also been processed by other softwares so I could compare). Now thinking about it I realise that the problem could be other than the file conversion. Does recon_all expect a particular convention (i.e. neurological/radiological) ? Thanks, Olivier Olivier Coulon wrote: Hi everyone, but then, when I do mri_convert -it analyze -i subject -o subject.mgz, the volume is shifted to one side (in addition to left/right swapped). If you look at the coronal sections I'm attaching, you see that a piece of ear the right ear is appearing at the left. I also have this problem of left/right inversion and I cannot figure out why this happens. Do we have to specify a --out_orientation string ? Thanks, Olivier -- --- Olivier Coulon, Chargé de Recherche CNRS Laboratoire LSIS, UMR CNRS 6168 Equipe IM, ESIL Campus de Luminy - Case 925, 13288 Marseille cedex 09 - France Tél: +33 (0)4 91 82 85 27Fax: +33 (0)4 91 82 85 51 email: [EMAIL PROTECTED] http://olivier.coulon.perso.univmed.fr --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] convert mnc-analyze-mgz
Doug Greve a écrit : How do you know it is left-right swapped? What tool are you using to visualize it? Do you have a fiducial? Hello, the surface reconstruction (visualised with scuba) gave a left hemisphere that should be the right one (I am using icbm data that have also been processed by other softwares so I could compare). Now thinking about it I realise that the problem could be other than the file conversion. Does recon_all expect a particular convention (i.e. neurological/radiological) ? Thanks, Olivier Olivier Coulon wrote: Hi everyone, but then, when I do mri_convert -it analyze -i subject -o subject.mgz, the volume is shifted to one side (in addition to left/right swapped). If you look at the coronal sections I'm attaching, you see that a piece of ear the right ear is appearing at the left. I also have this problem of left/right inversion and I cannot figure out why this happens. Do we have to specify a --out_orientation string ? Thanks, Olivier -- --- Olivier Coulon, Chargé de Recherche CNRS Laboratoire LSIS, UMR CNRS 6168 Equipe IM, ESIL Campus de Luminy - Case 925, 13288 Marseille cedex 09 - France Tél: +33 (0)4 91 82 85 27Fax: +33 (0)4 91 82 85 51 email: [EMAIL PROTECTED] http://olivier.coulon.perso.univmed.fr --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] convert mnc-analyze-mgz
Hi everyone, but then, when I do mri_convert -it analyze -i subject -o subject.mgz, the volume is shifted to one side (in addition to left/right swapped). If you look at the coronal sections I'm attaching, you see that a piece of ear the right ear is appearing at the left. I also have this problem of left/right inversion and I cannot figure out why this happens. Do we have to specify a --out_orientation string ? Thanks, Olivier -- --- Olivier Coulon, Chargé de Recherche CNRS Laboratoire LSIS, UMR CNRS 6168 Equipe IM, ESIL Campus de Luminy - Case 925, 13288 Marseille cedex 09 - France Tél: +33 (0)4 91 82 85 27Fax: +33 (0)4 91 82 85 51 email: [EMAIL PROTECTED] http://olivier.coulon.perso.univmed.fr --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
