Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

Job posting: 2-year postdoctoral position
by Scott Love 13 Sep '18

13 Sep '18

External Email - Use Caution Enquires and applications to Dr. Martine Migaud (Martine.Migaud(a)inra.fr) Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-year postdoctoral position is available in the group of Dr. Martine Migaud, at the laboratory of Reproductive and Behavioral Physiology (https://www6.val-de-loire.inra.fr/physiologie_reproduction_comportements) which brings together over 50 researchers from INRA, CNRS, the University of Tours and the French horse and riding institute (IFCE). Context and mission: The Project is part of a recently awarded grant from the French National Agency for Research and involves magnetic resonance imaging (MRI) analysis in a large animal model (sheep). This project aims to explore through MRI approaches, the mechanisms of brain plasticity in the hypothalamus, a structure involved in the control of reproduction. In this project, we aim to develop MR acquisition and post-processing methods to monitor brain changes and to obtain imaging biomarkers, based on the use of multi-modal neuro-imaging tools to investigate anatomical, connectivity and hypothalamic microstructure variations in function of the environment. Our lab makes use of sheep as an in vivo model system and for in vitro immunohistochemical and molecular approaches. The recruited post-doc will have access to the CIRE platform within the laboratory, dedicated to applied surgery and imaging of large animal models. The platform is equipped with state of the art imaging facilities including a clinical MRI scanner (3T Verio, Siemens) and a CT-Scanner (https://www6.val-de-loire.inra.fr/cire/Imagerie) He/she will also benefit from a strong collaborative local environment formed by the members of the CIRE platform and other scientists from our unit. In addition, the project is carried out in collaboration with the Team Development & Plasticity of the Neuroendocrine Brain, INSERM U1172, directed by Dr. V. Prévot. The position is available for two years and would ideally start in October 2018. Place: The laboratory is located in Nouzilly, in close proximity to Tours, in the heart of the Loire Valley, France. Tours is a pleasant city from which one can also reach Paris or Bordeaux very easily within 1h00 and 2h00 respectively by high-speed train. Candidate profile: The successful candidate will have a PhD in neuroscience, Electrical or Biomedical Engineering, or related fields with strong experience in MRI neuroimaging and in statistical analysis. Knowledge and previous experience in computer programming and analysis software (eg. Python, Matlab, C++, FSL, Freesurfer, Linux, Perl…) is mandatory. We are looking for a highly enthusiastic and autonomous candidate who can develop his/her line of research with an interest in interdisciplinary research and excellent interaction and communication skills in the context of a collaborative teamwork. To apply, please send by e-mail, your C.V., a motivation letter and the names and contact information of two referees to Dr. Martine Migaud (Martine.Migaud(a)inra.fr) We will consider applications until October 31, 2018.

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Optseq PSDWindow
by Leavitt, Mackenzie 12 Sep '18

12 Sep '18

External Email - Use Caution Hi, We are attempting to use optseq2 for a study design where the events last 5 seconds. ? I've found previous answers that indicate that PSDWIN max should be set between 21 to 24 seconds if your event is 3 seconds in length. For 5 seconds in length, I assume this would be between 25 and 30? My actual question is this: how does one determine the length of the hemodynamic response function and set their PSD max? Is there a heuristic you can use? Best, MacKenzie =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Problem to download dev version
by stdp82＠virgilio.it 12 Sep '18

12 Sep '18

External Email - Use Caution I'm tryining to download the Development Version (OSX) at: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall When I click on "here", I push the "guess" botton but the operation is failing. What do I do? Thanks Stefano

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Pre SFN Workshop Nov 2-3, 2018: Hands-on Reproducible Analysis of Neuroimaging Data
by Satrajit Ghosh 12 Sep '18

12 Sep '18

External Email - Use Caution *Hands-on Reproducible Analysis of Neuroimaging Data* *A ReproNim Pre-SFN 2018 Training Workshop* *Register here: https://tinyurl.com/repronim-sfn18 <https://tinyurl.com/repronim-sfn18>* Purpose: An increasing body of evidence point to some issues in reproducibility in biomedical or life sciences, raising concerns in the scientific community. ReproNim has developed a curriculum <http://www.reproducibleimaging.org/#training> that will give the students the information, tools and practices to perform repeatable and efficient research and a map of where to find the resources for deeper practical training. This training workshop will introduce material on the key aspects of reproducible brain imaging and will orient attendees using a hands on and practical experience to conduct neuroimaging analyses, using the next generation of tools. By the end of this course, the student will be aware of training materials and concepts necessary to perform reproducible research in neuroimaging. The student will be able to reuse these materials to conduct local workshops and training and be able to customize the training for their specific scenario. Prerequisites: If you are a student, postdoc or researcher in life science who directly works with neuroimaging data - or wish to work with these data, and you have some basic computational background, *this training workshop is for you*. You should have already done either some R, or Python, or Matlab or Shell scripting, or have used standard neuroimaging tools (SPM, FSL, Afni, FreeSurfer, etc) and be engaged in a neuroimaging research project. You should have already completed a neuroimaging analysis or know how to do one. Modules:Module Reproducibility Basics: Friday Nov. 2. 9am-10:45am. This module guides through three topics, which are in the heart of establishing and efficiently using common generic resources: command line shell, version control systems (for code and data), and distribution package managers. Gaining additional skills in any of those topics will help you to not only become more efficient in your day-to-day research activities, but also would lay foundation in establishing habits to make your work more reproducible. Module FAIR Data: Friday Nov. 2. 11am-12:45. This module provides an overview of strategies for making research outputs available through the web, with an emphasis on data. It introduces concepts such persistent identifiers, linked data, the semantic web and the FAIR principles. It is designed for those with little to no familiarity with these concepts. More technical discussions can be found in the reference materials. Module Data Processing: Friday Nov. 2. 2pm-3:45pm. This module teaches you to perform reproducible analysis, how to preserve the information, and how to share data and code with others. We will show an example framework for reproducible analysis, how to annotate, harmonize, clean, and version brain imaging data, how to create and maintain reproducible computational environments for analysis and use dataflow tools to capture provenance and perform efficient analyses (docker) and other tools. Module Statistics: Friday 4pm-5:15pm The goal of this module is to teach brain imagers about the statistical aspects of reproducibility. This module should give you a critical eye on the current literature and the knowledge to do solid statistical analysis, understand the limitations of p-values, the notion of power and of positive predictive values and how to represent evidence for results. Reproducible publication project - Saturday 9am-12:00 This is an hands on session: small groups will work with the instructors on the steps to deliver a fully reproducible publication. Logistics: *Location*: University of California San Diego (detail of location will be given by email) *Dates*: November 02-03, 2018. *How to register*: *https://tinyurl.com/repronim-sfn18 <https://tinyurl.com/repronim-sfn18>* *Costs*: 25$. *Schedule*: * Friday November 2nd:* 8:30-9am: Introduction to the course and participants “setup” 9am-10:45: Reproducibility Basics 10:45-11am : Coffee break 11am-12:45: FAIR data 12:45-2pm : Lunch+coffee 2pm-3:45: Data Processing 3:45-4pm: coffee break 4pm-5:15pm: Statistics for reproducible analyses * Saturday November 3rd:* 9am-9:30: Questions and answers and feedback session 9:30-12pm: The Re-executable Micro Publication Challenge During this time, we will propose a small challenge around producing an entirely re-executable neuroimaging analysis from fetching data to producing statistical results. This will also be a time with close interactions with neuroimaging experts in data handling and analysis. 12pm-12:30: Closing session: feedback and future: “become a trainer”. *Online office hours will be held prior to the workshop. Registered attendees will receive information via email.* *Instructors: *J. Bates, S. Ghosh, J. Grethe, Y. Halchenko, M. Hanke, C. Haselgrove, S. Hodge, D. Jarecka, D. Keator, D. Kennedy, M. Martone, N. Nichols, S. A. Abraham, J.-B. Poline, N. Preuss, M. Travers, and others *This workshop is brought to you by ReproNim: A Center for Reproducible Neuroimaging Computation NIH-NIBIB P41 EB019936*

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Minimum FS version for thalamic segmentation
by Niels Bergsland 12 Sep '18

12 Sep '18

External Email - Use Caution Hi Eugenio, Just a quick question - is there a minimum version of FS that is required to run the thalamic nuclei segmentation? I am just thinking about some old datasets that we have that were run with FS 5.1. Thanks and best wishes, Niels

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questions about trac-all -stat
by 薛倩雯 12 Sep '18

12 Sep '18

External Email - Use Caution Dear experts,I have some questions about along-path analysis: (1)how to determine the first position and last position of all subjects' pathway when converting all pathstats.byvoxel.txt files to a table for group analyses? (2)how to complete correspondence of points between subjects? (3)what is values in table for group analyses,diffusion measure of center or something else? Thanks! Qianwen

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Amygdala subfields segmentation
by Miguel Ángel Rivas Fernández 12 Sep '18

12 Sep '18

External Email - Use Caution Hi Freesurfer developes, I am trying to execute the hippocampal and amygdala segmentation command " segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" but freesurfer gave to me this error *command not found. * However, when I use the command that segment only the hippocampal subfields (recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>) I don´t have any problem. What would be the reason? Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández*

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Using the new Thalamus tool
by Erik O'Hanlon 12 Sep '18

12 Sep '18

External Email - Use Caution Hi FS Experts I've run my data through the brainstem, hippocampus and amygdala following the usual Recon_all and using the developmental version downloaded and stalled around Jan2018. I'd like to use the new thalamus tool and am wondering if I need to do a full install of the latest DEV version to do so. As I am still working on certain aspects of the analyses I've run so far, I don't want to overwrite my main FS installation mid analysis. Is it possible to download the toolbox and add it to my current dev version or is it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again? Thanks and regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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Latest dev version
by stdp82＠virgilio.it 12 Sep '18

12 Sep '18

External Email - Use Caution Please could you send me the link to download the the dev version with thalamus segmentation? Thanks Stefano

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strange eTIV values
by Miguel Ángel Rivas Fernández 11 Sep '18

11 Sep '18

External Email - Use Caution Hello Freesurfer experts, When I exported the Destrieux and Desikian-Killiany volume values from Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as follows: 101,632,104,008.0000 134,253,072,953.0000 155,967,056,944.0000 142,085,122,028.0000 181,105,664,397.0000 118,051,287,519.0000 896,135,067,103.0000 With how many decimals Freesurfer exports the eTIV values ?, that is, what is the precision of this measure? I do not know how many decimals this measure has. Another doubt, it is necessary to make some kind of numerical transformation on the eTIV values before including it as a covariate in the statistical analysis (for example, a logarithmic transformation). Best, -- *Miguel Ángel Rivas Fernández*

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Freesurfer September 2018