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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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Segmentation of thalamic nuclei - FreeSurferColorLUT
by stdp82＠virgilio.it 11 Sep '18

11 Sep '18

External Email - Use Caution Hi list, where can I find the list of regions that I obtain by trough the segmentation of thalamic nuclei? Are they in FreeSurferColorLUT? Which are the codes for right and left regions? Thanks Stefano

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Re: [Freesurfer] thalamic segmentation
by Vinny K 10 Sep '18

10 Sep '18

External Email - Use Caution Hi, I ran recon-all to generate the required files for the thalamic segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the latest development version of Freesurfer (06/09/2018) linux-cent06. The segmented thalamic nuclei were visualized but I could not find a table listing the thalamic nuclei and its associated label to help identify the specific nuclei. Any help would be greatly appreciated. Thanks, Vinny

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Head circumference of fsaverage?
by Gladia Hotan 10 Sep '18

10 Sep '18

External Email - Use Caution Hi, What is the head circumference of the fsaverage subject? Thanks and Best, Gladia

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