Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

mri_segment WM/GM limits
by Jonathan Holt 04 Nov '13

04 Nov '13

HI experts, I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? Jon

3 8

Inaccurate white matter and pial surfaces
by Linda Zhang 04 Nov '13

04 Nov '13

Dear all, A few of my subjects end up with surfaces where the white matter surface is actually the pial surface, probably due to less than ideal contrast between the wm and cortical gm. The aseg seems to do a better job though. I've attached a few images to demonstrate what I mean. What's the best method to correct this? I'm running FS 5.1 with the -nuintensitycor-3T flag for recon-all. Cheers, Linda

2 1

Research Felow/Postdoc: Neuroimaging in Cerebrovascular Disease
by Direktion, Institut f. Schlaganfall- und Demenzforschung 04 Nov '13

04 Nov '13

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 45 specialized hospitals, departments and institutions harboring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research at the Ludwig Maximilian University of Munich offers: Research Fellow/Postdoc: Neuroimaging in Cerebrovascular Disease (m/f) RESEARCH FOCUS and RESPONSIBILITIES: The research fellow/postdoc will work on the mechanisms of post-stroke dementia using multimodal MRI data acquired through a prospective longitudinal study that involves repeat structural and functional MRI together with amyloid PET and detailed cognitive testing. The project is funded by the German Center for Neurodegenerative Diseases (DZNE) and embedded in an ambitious imaging program on vascular cognitive impairment. The fellow/postdoc will work in a highly dynamic neuroimaging team and is encouraged to bring in own research ideas. REQUIREMENTS: The candidate should hold a PhD, MD or equivalent degree in relevant disciplines (informatics, engineering, mathematics, neuroscience), should be familiar with state of the art structural and functional imaging techniques and should have skills in image postprocessing. Solid knowledge of programming and statistics is a plus. An enthusiastic, reliable and independent work style will provide a good fit for our team. OFFER: We offer an excellent multidisciplinary environment with expertise in neuroimaging, neuropsychology, bioinformatics, epidemiology and state of the art multimodal neuroimaging equipment (3T MRI, high-density fMRI compatible EEG, molecular PET, IT infrastructure). The research team is embedded in the Munich Cluster for Systems Neurology, which is funded by the German Excellence Initiative. The research fellow will draw on a comprehensive database and technical support to facilitate efficient work conditions. He/she will work in a friendly, highly productive team at the Institute for Stroke and Dementia Research. The Ludwig Maximilian University of Munich (LMU) (http://www.en.uni-muenchen.de/index.html) Germany, and its hospitals figure among Germany's premier and internationally competitive biomedical research sites and are funded by the government's Excellence Initiative. Salary is according to TV-L. The position is limited for two years, with a possible extension. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can not be refunded. HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Prof. Dr. Martin Dichgans Marchioninistr. 15 81377 Munich | Germany Send application by email to: isd(a)med.uni-muenchen.de --------------------------- Viele Grüße Lilo Thomas Assistentin der Institutsleitung Institut für Schlaganfall- und Demenzforschung (ISD) Klinikum der Universität München Heiglhofstraße 55 D-81377 München Telefon: +49 (0)89 7095 - 7801 Fax: +49 (0)89 7095 - 8729 E-Mail: lilo.thomas(a)med.uni-muenchen.de<mailto:lilo.thomas@med.uni-muenchen.de> Internet: www.isd.klinikum.uni-muenchen.de<http://www.isd.klinikum.uni-muenchen.de/>

1 0

Betreff: Error “mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file”
by jana dinges 04 Nov '13

04 Nov '13

2 1

minimal freesurfer pieces for recon-all
by Satrajit Ghosh 04 Nov '13

04 Nov '13

hi folks, has anybody on this list: a. built or extracted the necessary pieces (binaries, libraries, atlases) for running vanilla recon-all only? b. or better still, has a package file for any linux distro? i know the neurodebian folks are building one, but that's not fully ready yet. cheers, satra

1 1

Whole brain tractography using Freesurfer surfaces as seed and target
by Karen Marie Sandø Ambrosen 04 Nov '13

04 Nov '13

Hi Freesurfer experts, I am trying to perform whole brain tractography using FSL's Probtrackx2 with Freesurfer white surfaces as seed and pial surfaces as targets. To obtain a whole brain connectivity graph I need the streamlines between the hemispheres. This means that I need to remove the part of the medial wall between the hemispheres corresponding to corpus callosum and anterior and posterior commissures. One possible solution might be to use mri_surf2vol to transform the white surfaces to volumes and hereafter multiply by corpus callosum and anterior and posterior commissures to cut holes in the white surface. After removing the relevant parts the volume is transformed back to a surface which is used as input to the tractography. I don't know if this is the best way to do it or if there is a better way to automatically obtain the whole brain white/pial surface? Any thoughts and comments are highly appreciated. Best, Karen

1 0

unilateral hippocampus segmentation fail
by Andreas Berger 04 Nov '13

04 Nov '13

Hi FreeSurfers, i came across a few subjects in which FreeSurfer 5.3 failed to properly label most of the hippocampus in one hemisphere. Specifically, it is the left hippocampus in all of the 5 cases in which this occured. The subjects are young, healthy, and without any anatomical peculiarities. Segmentation was fine in these subjects with FreeSurfer 5.1. Screenshots of one of these subjects are attached. regards, Andreas

1 0

difference in atlas size
by Satrajit Ghosh 03 Nov '13

03 Nov '13

hi i noticed a big discrepancy in size between these two, but not among other lh and rh gcs files. > 28769857 May 13 17:21 rh.DKTatlas100.gcs > 6883965 May 13 17:21 lh.DKTatlas100.gcs are these the intended sizes? this is from the 5.3 centos6_x86_64 distro cheers, satra

1 0

ERROR: could not find ribbon.mgz
by jana dinges 03 Nov '13

03 Nov '13

1 0

Image acquisition in different head coils
by carolina.mr 02 Nov '13

02 Nov '13

2 1

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Freesurfer November 2013