Freesurfer

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Postdoc Position in Computational Neuroscience, Max Planck Institute, Leipzig, Germany
by Katharina von Kriegstein 13 May '16

13 May '16

Applications are welcomed for a postdoctoral research position at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany in collaboration with the Technical University Dresden, Germany. The objective of the postdoctoral research project is to use computational modelling and neuroimaging to work towards a novel model for cortico-subcortical interactions for human communication signals. The project is funded by the ERC-consolidator grant SENSOCOM (http://cordis.europa.eu/project/rcn/199655_en.html) The position will be jointly supervised by Katharina von Kriegstein at the MPI-CBS and Stefan Kiebel at the TU Dresden. The MPI-CBS offers a unique research environment with a 7.0 T MRI scanner, several 3.0 T MRI scanners, a 306 channels MEG system, TMS/tDCS laboratories, several EEG suites, and eye-tracking labs. All facilities and data analyses are supported by experienced IT specialists and physicists. The TU Dresden is one out of eleven German Universities of Excellence. It houses a state-of-the art neuroimaging centre with a strong focus on computational modelling and access to the TU Dresden high-performance computing clusters. Besides an excellent infrastructure, both centres offer an international and friendly environment with researchers from diverse backgrounds. The position is ideal for candidates interested in research at the interface between computational modelling and experimental neuroimaging. The candidates must have a PhD (or equivalent) in computational neuroscience, experimental psychology, or a related field, and should be able to demonstrate a consistently outstanding academic record, including publications. The ideal candidate will have expertise in computational neuroscience, physics, mathematics, or similar with a strong interest in implementing computational models (e.g., Bayesian filtering, hierarchical dynamic models, predictive coding) and testing these with neuroimaging experiments. The starting date for the position is flexible. Initially for two years, the position offers the possibility of extension for up to four years. Salary depends on experience and is based on regulations of the Max Planck Society. To apply, please include all documents in one PDF-file in the following order: CV, contact information of two referees, a brief statement describing your personal qualifications and future research interests, copies of up to three of your publications. Applications with the subject heading "CM 16 PD" should be sent via email to: personal(a)cbs.mpg.de. Closing date for applications is the 12th June 2016. Informal enquiries regarding the post should be directed to: Prof. Dr. Katharina von Kriegstein (kriegstein(a)cbs.mpg.de) For more information about the groups see: Prof. Katharina von Kriegstein: http://www.cbs.mpg.de/independent-research-groups/human-communication Prof. Stefan Kiebel: https://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_n… A link to the position description is available here: http://www.cbs.mpg.de/454795/job_full_offer_10498685?c=7390 The MPI-CBS is an equal opportunities employer, committed to the advancement of individuals without regard to ethnicity, religion, gender, or disability. --- Katharina von Kriegstein Max Planck Research Group Leader Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Professor of Cognitive and Clinical Neuroscience Humboldt University of Berlin Rudower Chaussee 18, 12489 Berlin, Germany Phone +49 (0) 341-9940-2476 Fax +49 (0) 341-9940-2448 http://www.cbs.mpg.de/independent-research-groups/human-communication

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Re: [Freesurfer] Manual correction for brainstem module
by Jacky Lee 13 May '16

13 May '16

Hi Eugenio, Yes please give me some advice on the matlab commands for this since I am not very familiar with matlab... Cheers, Jacky Hi Jacky, this is a good question, and unfortunately there isn't a great answer to it. The volume is computed upong a probabilitic segmentation of the voxels that is not written to disk (this is very similar to what happens with aseg.mgz and aseg.stats). In order to properly update the volume estimates, you would have to know the probability that the inpainted voxels belong to the brainstem as estimated by the algorithm, which we don't currently write to disk. Another option would be to toss the volumes given by the algorithm, and compute new volumes for all cases and brainstem structures using the hard segmentations. You would simply have to count the number of voxels labeled as midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. with Matlab (let me know if you need help with this). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" <cyle...(a)gmail.com> To: "Freesurfer support list" <Freesurfer(a)nmr.mgh.harvard.edu> Sent: Monday, May 9, 2016 2:01:53 AM Subject: [Freesurfer] Manual correction for brainstem module Hi freesurfer experts, I have successfully run the brainstem module for some subjects. On visual checking, I can see there are voxels with T1 hypointense lesions mislabelled as non-brainstem tissue. I manually corrected them on the brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected volume of the brainstem substructures? Thanks. Regards, Jacky

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X graphics issues via SSH
by Rockers, Elijah D. 12 May '16

12 May '16

Hello freesurfers, Running a Mac Pro, OS X El Capitan 10.11.4 With ATI Radeon Graphics card, and XQuartz v 2.7.9 I am able to run Qdec and freeview perfectly fine on my machine. The problem comes when I attempt to SSH into another machine and use these programs (it used to work fine, but I am wondering if something in our configuration has changed now) I get the following errors [belen@picasso:~] freeview Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error: BadValue (integer parameter out of range for operation) 2 Extension: 150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) [belen@picasso:~] qdec Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1504 Current serial number in output stream: 1505 Based on my limited knowledge, It seems likely to be a problem with X / SSH, and the graphics card, but I am unsure on how to proceed from here. If anyone has any ideas on how to overcome this, I would be incredibly grateful. The server machine itself also has a monitor, and can run Qdec and Freeview fine locally, with no problems. the issue seems to happen over SSH Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties and designated as a Magnet hospital for excellence in nursing. Houston Methodist has also been named to FORTUNE® Magazine's "100 Best Companies to Work For®" list for 10 years in a row. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Volumetric Data Discrepancies
by Tamara Tavares 12 May '16

12 May '16

Hello All, I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all. I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies? I really appreciate your time and assistant with this issue. Thank you in advance for your help! Tamara

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Folding
by Caverzasi, Eduardo 12 May '16

12 May '16

Hello all, I am not sure my previous email was received. We are looking at developmental anomalies in children and we using Freesurfer to asses thickness, volume but also local gyration indexes, using QDEC tool but also extrapolating the actual values for correlations. The local gyration index by itself is not specific enough to characterize the pattern of folding. There are other metrics such as the folding index and gyration indexes available and we are thinking to use these metrics too, however I can find online exactly how these metrics are obtained and their meaning. Is there any other metric we should also consider? Best regards, Eduardo

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group roi to individual native functional
by Patrick Beukema 12 May '16

12 May '16

Hi, I am trying to register a volumetric roi from an average subject that I created to each individual subject's functional space. I have the transformation matrices that I applied to the functional data to bring them into the average space. When I apply the inverse of those transforms to the roi, the results are way off so I think I must be missing something. 1. I created a volume from a label with mri_label2vol. 2. I map the volume in the average space to the native functional space with mri_vol2vol. I take it this is not correct and would appreciate any guidance. Thank you, pb

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External Regressor of Interest in FS-FAST
by Mcnorgan, Christopher 11 May '16

11 May '16

The references to external regressors in mkanalysis-sess are a little sparse on how I would go about analyzing a continuous regressor: I have a mixed design experiment: TaskBlock1 Rest TaskBlock2 Rest … TaskBlockN Rest x6 Runs Within each block are jittered events (5 of condition A, 5 of condition B). A colleague of mine agreed that the A vs B contrast should be pretty robust even in a single participant (it’s an established paradigm), considering I have over 150 trials of each, but I am seeing nothing at any reasonable threshold in my single participant. My colleague suggested checking whether there were any regions with activity that increased/decreased as a function of block over the course of the experiment (essentially, a neural practice effect). Hypothetically, such a region would show a linear drift in activity across 6*N blocks, but only during the block periods (reverting to baseline during the rest periods). >From the mkanalysis-sess.new wiki page, it appears that the -extreg flag can be used to pass an additional regressor file, but it’s unclear from the rest of the description how to construct this file, nor how to view the GLM associated with this analysis. Thanks for your time; I’ll post the solution on my lab wiki once it’s all sorted out Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Announcing the the HCP Course 2016 in Boston Aug 28-Sept 1
by Jennifer Elam 11 May '16

11 May '16

The Human Connectome Project (HCP) is pleased to announce the 2016 HCP Course: “Exploring the Human Connectome” <http://humanconnectome.org/courses/2016/exploring-the-human-connectome.php>, to be held August 28-September 1 (Sunday-Thursday) at the Joseph B. Martin Conference Center <http://www.theconfcenter.hms.harvard.edu/> at Harvard Medical School, in Boston, Massachusetts, USA. This 5-day intensive course will provide training in the acquisition, analysis and visualization of whole-brain imaging and behavioral data from the Human Connectome Project (HCP) using methods and informatics tools developed by the WU-Minn HCP consortium plus data made freely available to the neuroscience community. The course is designed for investigators who are interested in: *using data being collected and distributed by HCP *acquiring and analyzing HCP-style imaging and behavioral data at your own institution *processing your own non-HCP imaging data using HCP pipelines and methods *learning to use Connectome Workbench tools and the CIFTI connectivity data format *learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data *positioning yourself to capitalize on HCP-style data from forthcoming large-scale projects (e.g., Lifespan HCP and Connectomes Related to Human Disease) Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data. Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. The course is open to graduate students, postdocs, faculty, and industry participants. The course is aimed at both new and existing users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including familiarity with FSL and Freesurfer software. For more info and to register visit the HCP Course website <http://humanconnectome.org/courses/2016/exploring-the-human-connectome.php>. We hope to see you in Bah-ston! Best, 2016 HCP Course Organizers

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Direction of bbregister transformation
by Michael Waskom 11 May '16

11 May '16

Hi Freesurfers, I have a question about the direction of the transformation written out to the register.dat file by bbregister. I have looked at the fscoordinates powerpoint presentation, which I think is telling me that this matrix actually maps from the orig.mgz RAS coordinates to the functional RAS coordinates. That agrees with the results I get when I try to use the matrix outside of Freesurfer. However, this is a little surprising, because I think of the bbregister process as aligning the functional (moving) with the anatomy (target) so I would have expected the transform matrix to represent that mapping. Can you please confirm whether my understanding of the fscoordinates presentation is correct, or help me out if I am off base? Thanks! Michael

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Normalization for functional connectivity
by Sahil Bajaj 11 May '16

11 May '16

Hello all, I am interested in importing some seed regions which are in MNI space in order to calculate functional connectivity maps. Looks like command preproc-sess doesn't normalize the BOLD data and only the regions generated by FreeSurfer LookUp table which have 'segid', can be used to calculate functional connectivity maps. I was wondering how can I normalize the BOLD and T1w data so that I can use http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… instructions to calculate functional connectivity from MNI seed regions. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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