[Freesurfer] postdoc position in Leiden, The Netherlands: studies on resting-state and activation EEG-fMRI during sleep and wakefulness in healthy subjects and patient with sleep disorders including i
LEIDEN UNIVERSITY MEDICAL CENTER The Leiden University Medical Center (LUMC) has initiated the interdisciplinary Sleep Neuroscience Center Leiden. Its focus is fundamental and strategic scientific and clinical research on sleep Within the Departments of Neurology and Neuroradiology, and in close collaboration with Dr. E.J.W. van Someren’s Sleep & Cognition group at the Netherlands Institute for Neuroscience, a position is available for a Postdoc (m/f) 38 hours per week Project information: This project is funded by a LUMC starting grant for the Sleep Neuroscience Center Leiden. It has become evident over the last decade that sleep is an essential component of normal cognitive functioning and maintenance of brain structure and function at the cellular to the systems level. In addition, disturbed sleep crucially contributes to major health problems associated with metabolic regulation, aging and psychiatry. The present project aims to elucidate the association between activatiion of the default mode resting state network, it’s structural backbone, and travelling slow oscillations during sleep. A second focus is on the involvement of the default mode network in deviant switching between sleep and wakefulness in narcolepsy and insomnia. Philips 7T and 3T scanners are available for structural and functional MRI. The aim is to do EEG-MRI with the new Electrical Geodesics Inc (EGI) system. The project will be performed in close collaboration with Dr. S. Rombouts (director of the Leiden Institute for Brain and Cognition: LIBC) and with the Sleep & Cognition group at the Netherlands Institute for Neuroscience. A 0.5 FTE lab technician will support the project. Requirements: A strong scientific track record including publications is essential for the Postdoc. The Postdoc will be responsible for studies on resting-state and activation EEG-fMRI during sleep and wakefulness in healthy subjects and patient with sleep disorders including insomnia and narcolepsy. Appoinment: This position involves a temporary appointment for three years. Salary: Depending on training and work experience according to the collective Agreement for Dutch Universities (CAO-Nederlandse Universiteiten), including 8% holiday pay and a 8.3% year-end bonus. We offer an extensive package of fringe benefits. Work location: The Leiden University Medical Center, Leiden. Information: For further information about this position, you may contact Dr. EJW Van Someren (e-mail e.van.some...@nin.knaw.nl) or Dr. SARB Rombouts (s.a.r.b.rombo...@lumc.nl ). Information on the groups is found at http://www.nin.knaw.nl/research_groups/van_someren_group/ and at http://www.libc-leiden.nl Application: You may send your application letter, curriculum vitae and the names of 2 references to Dr. EJW Van Someren (Laboratory for Neurophysiology, Department of Molecular Cell Biology, LUMC S-05-P, PO Box 9600, 2300 RC Leiden, The Netherlands) or preferably by email: e.van.some...@nin.knaw.nl. Application deadline: January 14, 2010. Any acquisition further to this advertisement will not be appreciated___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Wm/pial edits misclassification
Hi Lena, it's probably an incorrectly fixed topological defect. If you email me the wm.mgz and the lh.orig surface I'll take a look. cheers, Bruce On Sat, 12 Dec 2009, Lena Palaniyappan wrote: Hi all Please see the attached images slices 108 to 111 What is happening at precentral / middle frontal white matter? How should I be correcting this? The wm slices as you can see have missing volumes. I cannot fill these spaces in wm surface as there is no obvious white matter in the original surface. How should I go about correcting this? Many thanks in anticipation Lena ___ Lena Palaniyappan Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Co-registration in FS
Hi FSers, I am new to freesurfer. now start to use it for looking at struc-func relationship. Normally, in fsl, I employ bet for both example_func and highresh anat. it means that the func_brain and anat_brain are fed into flirt to estimate the co-registration. here, i try to use reg_feat2anat to do this. but in this new version (4.5), it told me the betfunc command can not be found. thus I just used the version without --bet. the results in tksurfer looked not good. I am guessing it was caused by the highres with large neck areas. MY QUESTION is how can I trigger reg_feat2anat (or whatever other commands) to take skull-stripped highres for the co-registration (in fact, the brainmask.mgz already there)? Or I was wrong, reg_feat2anat did this consideration? Any suggestions would be appreciated! -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: 212-263-4735 Public: www.AboutOurKids.org Academic: http://publicationslist.org/xinian.zuo Personal: zuoxinian.googlepages.com Blog: http://restbrain.blogspot.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] UC Berkeley RA position
Position in PET imaging at UC Berkeley/Lawrence Berkeley National Laboratory We're looking for a research assistant to work with multisite PET data. The position involves downloading PET images from archived sites, using existing software to extract numerical values from these images, analyzing data sets using values from these PET scans as well as associated clinical, demographic, cognitive, and biomarker data from databases of enrolled subjects. Education/Training: BA or BS preferably in neuroscience, engineering related fields, or psychology Skills: Familiarity with medical images and techniques used for image analysis, familiarity with multiple operating systems (Linux, Unix, OSX, Windows), familiarity with statistics (SPSS, R, etc.), experience in working with PET or MR images in SPM, FSL, and/or other analysis program, programming experience in Matlab or Python, experience working with databases Please apply online here (JOB ID#10185): http://jobs.berkeley.edu/ Jagust Laboratory Helen Wills Neuroscience Department, UC Berkeley Lawrence Berkeley National Laboratory ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error: cannot open libXss.so.1?
Dear Freesurfer,
I ran recon-all with -all flag,
and I've got an error message as below:
>mris_volmask.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
>Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24 20:07:49
EDT 2008 i686 i686 i386 GNU/Linux
>recon-all exited with ERRORS at Tue Dec 8 07:43:35 KST 2009
I ran it on {Intel(R) Xeon(R) CPU E5345 @ 2.33GHz (4096 KB cache)}
with {Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24
20:07:49 EDT 2008 i686 i686 i386 GNU/Linux}
I've googled it, only one case was posted via this mailing list.
Yes, I want to know why this error occur but also how to fix it.
Please help me out here! 'A`
Mr. SG KIM.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error: cannot open libXss.so.1?
i'm guessing from the 'compute-0-1.local' bit of your output that this
was run on cluster, which probably doesnt have the X-libs installed
(clusters generally dont include the graphics libs). unfortunately, our
mris_volmask is built against a VTK lib which relies upon linking
against these (even though it doesnt use them: VTK is primarily a
visualization lib, but has some very useful volume/surface routines as
well). the only short-term solution for you is to use
mris_volmask_novtk, which is an alternate binary that doesnt use vtk,
but doesnt produce nearly the quality cortical ribbon that VTK does.
but it will have to do (and is irrelevant if you need only the cortical
and subcortical data: the volmask is used only the create the aparc
+aseg.mgz and wmparc.mgz files).
for the long-term, we are working on a replacement to mris_volmask that
doesnt use the VTK lib, but produces identical (or nearly so) results.
this wont appear for a couple more months though.
n.
On Sun, 2009-12-13 at 10:57 +0900, SG KIM wrote:
> Dear Freesurfer,
> I ran recon-all with -all flag,
> and I've got an error message as below:
>
> >mris_volmask.bin: error while loading shared libraries: libXss.so.1:
> cannot open shared object file: No such file or directory
> >Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24
> 20:07:49 EDT 2008 i686 i686 i386 GNU/Linux
> >recon-all exited with ERRORS at Tue Dec 8 07:43:35 KST 2009
>
> I ran it on {Intel(R) Xeon(R) CPU E5345 @ 2.33GHz (4096 KB cache)}
> with {Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24
> 20:07:49 EDT 2008 i686 i686 i386 GNU/Linux}
>
>
> I've googled it, only one case was posted via this mailing list.
> Yes, I want to know why this error occur but also how to fix it.
>
>
> Please help me out here! 'A`
>
>
> Mr. SG KIM.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
