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post-doctoral position at MRC Cognition and Brain Sciences Unit, Cambridge
by Olaf Hauk 13 Jul '16

13 Jul '16

MRC Cognition and Brain Sciences Unit - Cambridge Postdoctoral Scientist Salary £27,355 - £30,791 per annum plus benefits Ref OH/260 The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute of cognitive neuroscience. Onsite facilities include dedicated MRI and MEG scanners, a hearing laboratory, and the developmental research centre suitable for infants through to older children. The CBSU is also a stakeholder in a clinical research facility and a new 7T ultra high field MRI scanner on the Addenbrooke's campus in Cambridge. An open-ended post-doctoral position is available in the Methods Team to support the optimisation, standardisation and development of fMRI data analysis pipelines, e.g. for standard fMRI time series analysis, functional and effective connectivity analysis, and multivariate pattern analysis. Methods support may extend to EEG/MEG analysis where appropriate. The successful candidate will also participate in a skills-oriented neuroimaging training programme aimed at PhD students and post-doctoral researchers. The position offers scope for independent research and methods development. You will have, or be in the final stages of, a PhD related to physics, signal processing, or neuroimaging methods. You should have experience in fMRI analysis, scientific computing (e.g. Linux, Matlab, Python), and an appreciation of methodological issues in cognitive brain imaging. Experience with MRI data acquisition and EEG and MEG methodology would be desirable. You will be thorough, efficient, effective, a good communicator, and enjoy working as part of a diverse and energetic, interdisciplinary team. Choosing to come to work at the MRC CBSU means that you will have access to a whole host of benefits from a final salary pension scheme, 30 days annual leave entitlement, flexible working arrangements, childcare vouchers, and additionally a salary sacrifice cycle scheme, as well as access to employee/shopping travel discounts. On site car and bicycle parking is available. We also provide a wide range of training opportunities to all our staff. Our success is dependent on our ability to embrace diversity and draw on the skills, understanding and experience of all our staff. As holders of an Athena SWAN bronze award we welcome applications from all sections of the community irrespective of gender, race, ethnic or national origin, religion or belief, sexual orientation, disability or age. As users of the "Two Ticks" disability symbol we guarantee to interview all applicants with disabilities who meet the minimum essential criteria for the post. For full details of this post and to complete an online application form visit https://mrc.tal.net/vx/lang-en-GB/appcentre-1/candidate/postings/280 and upload your CV along with a covering letter stating why you are applying for the post. Closing date: 9th August 2016 [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> This position is subject to pre-employment screening The Medical Research Council is an Equal Opportunities Employer Olaf Hauk, PhD MRC Cognition and Brain Sciences Unit Phone: +44(0)1223 273702 Fax: +44(0)1223 359062 Web: http://www.mrc-cbu.cam.ac.uk/people/olaf.hauk/

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TRACULA tract group comparison p-values
by Barbara Kreilkamp 13 Jul '16

13 Jul '16

Dear Freesurfers, I am looking for a way to add a colorbar to my p-value tract cores generated through TRACULA. When I load up the images as described in the tutorial here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and there is no option to select my textfile with the p-values unfortunately. Would you please help? Thanks ever so, Barbara

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FreesurferNHP
by Lauro, Peter 12 Jul '16

12 Jul '16

Hello, I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I tried following the instructions/scripts listed here ( https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) but I was unable to make it work (I'm also running FS 5.3). I noticed on the Washington-Pipelines github FAQ page listed a FreesurferNHP pipeline ( https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-wan…) but it hasn't been released yet. Do you know when this pipeline will be available? Alternatively, is there another way I can obtain the pipeline scripts and template volumes? Thank you, Pete Lauro

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ERROR reading /..../label/lh.BA1.label
by Uquillas, Federico D'Oleire 12 Jul '16

12 Jul '16

Dear fellow FreeSurfer users, My jobs fail at the the last mri_label2label step of -autorecon3, and I cannot figure out why. Any help or input would be greatly appreciated. I am attaching a recon-all log for two of these subjects. The error says that it's not possible to read the labels contained in the fsaverage/labels/ folder. These labels/files do exist however if you look in the /labels/ folder. I'm using Centos 6.7 (Final) Kernel Linux 2.6.32-573.22.1.el6.x86_64 GNOME 2.28.2 My username is fdu0. A path to my most recent error fail can be the following: /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 (PBS Job ID: 11918069) another one with this same error fail is /FreeSurferProc/AD08 (PBS Job ID: 11914847). Thank you very much for your time and any help you may be able to provide. Fred

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Fwd: TRACULA stat extraction issue
by Shashwath Meda 12 Jul '16

12 Jul '16

Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath

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Freeview question
by pfotiad＠nmr.mgh.harvard.edu 12 Jul '16

12 Jul '16

Hello FS Community, Lately, whenever I am trying to use freeview I get the following error message: freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Exit 127 The error started showing up after the cluster went down. I was wondering whether there was a way to fix this since I don't have admin privileges (and hence can't sudo). Thanks in advance, Panos

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Slight rotation when viewing brainmask.mgz in Freeview - why and is this a cause for concern?
by Reema Jayakar 12 Jul '16

12 Jul '16

Hello FS developers/users, When viewing brainmask.mgz in Freeview, for some subjects the brain is slightly (~10-20 degrees) rotated. By looking at the raw data, I see that their head position in the scanner was slightly skewed. I thought that brainmask.mgz is created after Talairach transformation and normalization has been completed. I took this to mean that the brainmask.mgz file has been registered to an atlas. If so, shouldn't the brainmask.mgz files for all subjects appear with 0 rotation in freeview? Should I be concerned that this is not the case for my dataset? Thanks for your help! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

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Visually inspecting subcortical segmentations + what command should be run to apply manual fixes to aseg.mgz voxels?
by Reema Jayakar 12 Jul '16

12 Jul '16

Hello FS developers/users, I have a two part question regarding subcortical segmentation: 1) To visually inspect if segmentation accurately captures structure boundaries (e.g., amygdala) I am using the norm.mgz file and overlaying it with the aseg.mgz file in Freeview. Is this correct? Or should I be using brainmask.mgz (instead of norm.mgz)? Also, Freeview gives me some options - "Resample to standard RAS space" and "Apply registration file". Where can I find information about whether or not to use these options? 2) If I manually edit the boundaries of the amygdala (either by erasing voxels or using the color brush to add voxels), what command should I use to re-run such that the corrections are applied to my aseg.stats output? The command I found on the wiki page says to use recon-all -autorecon-2-noaseg -subjid <Subj_ID>. My understanding was that the -noaseg flag will skip all the subcortical segmentation steps and that is not what I want. What I want is for FS to re-run subcortical segmentation such that it reflects the voxel editing I did in Freeview. This is the first time I am doing something like this so any help you can provide or pointing me to the right resource would be great! Thank you! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

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mri_glmfit-sim
by Lauri Tuominen 12 Jul '16

12 Jul '16

Dear Freesurfers, As freesurfer mri_glmfit-sim is based on AlphaSim & FSL randomise, I would like to know if the results I’m getting are affected by recently found bugs/violations in RFT assumptions, e.g. http://www.pnas.org/content/early/2016/06/27/1602413113.full.pdf. Thank you in advance! Lauri Tuominen

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tcsh update
by shi yao wang 12 Jul '16

12 Jul '16

Dear FS experts: I am running FS in local computer and showing following error message and program stopped at recon-all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Do I need to update tcsh? and how can I do it. thanks Lawrence

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