[Freesurfer] Postdoctoral Fellowship in multimodal developmental neuroimaging
Postdoctoral Fellowship in multimodal developmental neuroimaging Applications are invited for a 2-years postdoctoral fellowship in the human multimodal neuroimaging project Linking the major system markers for typical and atypical brain development: a multimodal imaging and spectroscopy study (http://www.zihp.uzh.ch/1610.php#45) funded by the Zürich Institute of Human Physiology. This study will investigate the major physiological markers of brain development, using a combination of advanced magnetic resonance imaging (e.g., functional MRI) and MR-spectroscopy methods. The initial phase of the study will establish baseline neurotransmitter levels, cerebral blood flow (e.g., perfusion MRI) and EEG frequency and power at rest across a range of age groups. Examining the interactions between these markers and the changes they demonstrate with age and hormone levels will allow to better understanding the global and regional processes underlying brain maturation. The later phases will investigate changes in these physiological markers with (a) cognitive tasks and (b) attention deficit hyperactivity disorder (ADHD). The starting date of the position is January 2011. The successful applicant will have a PhD research background in Cognitive Neuroscience, Neurophysiology, Psychology, Neuropsychology, or related fields. Fluency in English, good oral and written German, and the ability to work within a multidisciplinary team are essential. Applicants should be experienced at conducting fMRI and/or EEG studies and be familiar with analysis software, such as SPM/Matlab, BrainVoyager and/or FSL. Experience with stimulus presentation software (such as Presentation), UNIX, and programming languages a plus. Salaries are in accordance with the Swiss National Research Foundation (starting at around 80'000 CHF p.a.). APPLICATION INSTRUCTIONS: To apply by e-mail (max 5 MB), please send a curriculum vitae, a personal statement describing research interests, 3 letters of recommendations, and up to 5 article reprints/preprints to: Dr Lars Michels lars.mich...@kispi.uzh.ch MR-Zentrum University Children's Hospital Steinwiesstrasse 75 Zürich 8032 Switzerland Reviews of applications will begin on the 7th of November and will continue until the positions are filled. ___ 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] Freeview and Mac OS 10.6 - Snow Leopard
it does not work in v5.0. however, this is one of our top priorities to get working for release in the upcoming 5.1 (within a month or less). n. On Fri, 2010-10-22 at 12:42 +0200, Andreas Schindler wrote: Dear Freesurfers Does anyone know if freeview already works on Mac OS Snow Leopard or when it will be patched? best wishes Andreas ___ 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 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] mni coordinates to volume index
Hi, Is it possible in matlab to get the volume index coordinates corresponding to specific MNI coordiates? Thanks, Yigal ___ 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] Talairach coordinates for Desikan gyral regions
the subject 'fsaverage', included in the subjects dir of the distribution, is already registered to talairach space, and it contains the desikan annotations, so you could get the coords from that. you'd have to load it in tksurfer and click on the center vertex of region to get the coord though, as there is no automated way to find the center of the region (that i know of). n. On Fri, 2010-10-22 at 16:03 -0400, Robustelli, Briana (NIH/NIMH) [F] wrote: Hi all, We are trying to depict spatial relations of each of the Desikan et. al (2006) gyral regions in a separate 3-D graph. To do this we need every regions' center Talairach coordinates in common space, not in relation to any particular group or subject. Is there a way to do this using Freesurfer? Thank you. Briana ___ 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 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] Nifti surface to FreeSurfer surface
Dear experts, I got BEM surfaces out of the BET tool from the FSL package. The surface files are in nifti format (*.nii.gz). Now I wonder if there is any opportunity to convert nifti surfaces to FreeSurfer surface in surf format (*.surf)? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander ___ 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] Nifti surface to FreeSurfer surface
use mri_binarize to set each brain voxel value to the same value (maybe bet does this), then use something like: mri_tesselate mybrainmask.nii.gz 127 mybrainmask.surf where '127' happens to be voxel value used in the binarization. n. On Fri, 2010-10-22 at 15:08 -0600, Alexander Hunold wrote: Dear experts, I got BEM surfaces out of the BET tool from the FSL package. The surface files are in nifti format (*.nii.gz). Now I wonder if there is any opportunity to convert nifti surfaces to FreeSurfer surface in surf format (*.surf)? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander ___ 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 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] data not Surving FDR
Hi, I have a dataset that seems to have some very nice group differences (please see the graph and qdec image), but they never seem to survive FDR. I noticed when I run the Set Using FDR, it generates a very high threshold above 5; where as, with some of my other datasets FDR is set much lower (often in the 2's and 3's). Can you please give me some insight into why the threshold is being set so high? Is it solely linked to the small sample size, or is there something additional we can do in the processing, so that regions with such large group differences will survive correction? Thank you, Mira ___ 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] data not Surving FDR
Hi Mira, If the map you provided is of uncorrected p-values at say p=0.05, then you appear to have just a couple small regions of group differences, so it isn't surprising that after FDR nothing would survive. The result is what it is, and unless you had specific a priori hypotheses regarding regions that would be involved (i.e., to which you could restrict your testing), then there isn't much you can do. cheers, -MH On Fri, 2010-10-22 at 14:53 -0700, Mira Michelle Raman wrote: Hi, I have a dataset that seems to have some very nice group differences (please see the graph and qdec image), but they never seem to survive FDR. I noticed when I run the Set Using FDR, it generates a very high threshold above 5; where as, with some of my other datasets FDR is set much lower (often in the 2's and 3's). Can you please give me some insight into why the threshold is being set so high? Is it solely linked to the small sample size, or is there something additional we can do in the processing, so that regions with such large group differences will survive correction? Thank you, Mira ___ 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
