Freesurfer

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30089 discussions

Cuda version > 5.0
by Melanie Ganz 08 Feb '18

08 Feb '18

Dear FS list, we just got a really nice graphics card (Quadro P6000) that we also would like to use to speed up recon-all, preferably for running high-res data with FS version 6. Now we know that in the precompiled FS version 6 it still looks for cuda 5.0, but it seems like some people have gotten it to work with 8.0 (see e.g. here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-May/052047.html) Has anyone gotten FS version 6 compiled with cuda 9.1? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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freesurfer segmentation: perirhinal Roi
by m.bahri＠uliege.be 08 Feb '18

08 Feb '18

Dear Freesurfer experts, We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin? Many thanks in advance, Best regards, -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.bahri(a)uliege.be Tel : + 32-4-3662304

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Re: [Freesurfer] Extending pial surface to include excluded cortex
by Arsenije Subotic 08 Feb '18

08 Feb '18

Hi Doug, I’ve noticed that in my right hemisphere on top (I’m only using this hemisphere as the other hemisphere has tissue loss due to ischemia) there is also some atrophy. However, I’ve noticed that the surface can still probably be extended. It seems that there are some wm voxels which connect and disconnect after a couple of slices when I have wm.mgz on top of brain mask and when I use the heat colormap. In this case, is it ok to add wm voxels to connect them to the wm.mgz volume? This is what the tutorial says I should do, but I am worried since the wm intensity is sometimes 0 between these detached wm voxels and the main wm voxel. You can see it on the top left corner. And in general if there is no white matter sometimes and the pial surface does not extend and there is no defect, what is the general protocol? Thank you for your help! Arsenije

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Extending pial surface to include excluded cortex
by Arsenije Subotic 07 Feb '18

07 Feb '18

Hi everyone, Is it possible to extend the pial surface in order to exclude some missing cortex, without adding control points? For one of my subjects I'm missing cortex for about 10-15 slices and I think control points should not be added. I've attached some screenshots that showcase the problem. Thanks for your help. Best, Arsenije

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brainGraph (graph theory analysis in R) major release: v2.0.0
by Chris Watson 07 Feb '18

07 Feb '18

Dear Freesurfer users, I am pleased to announce the 2nd major release of my R package for graph theory analysis of brain MRI data, "brainGraph". The main page on CRAN is at: https://cran.r-project.org/ web/packages/brainGraph/index.html The GitHub repository is at: https://github.com/cwatson/brainGraph *Installation* The latest version is already on CRAN for Linux distributions, and should be for Windows and Mac OS X soon (but there may be issues on non-Linux systems; see Chapter 1 of the User Guide). To install directly from CRAN: > install.packages('brainGraph') In the meantime (and for development versions), you may install from GitHub using the R package "devtools": > devtools::install_github('cwatson/brainGraph') *Getting help* The new User Guide has been completely overhauled, and now has a permanent link at: my GitHub Pages site (PDF warning) <https://cwatson.github.io/files/brainGraph_UserGuide.pdf>. Please start at the "Preface". You may also get help by opening an Issue <https://github.com/cwatson/brainGraph/issues> on the GitHub repository, or join the Google Group <https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>. *New features* You can find the release notes/changelog in NEWS.md, at: https://github.com/cwatson/brainGraph/blob/master/NEWS.md Major additions (since v1.0.0) that should be of interest include: - Vertex- and graph-level *mediation analysis* (chapter 11 of the Guide) - Multi-threshold permutation correction (MTPC) for GLM analyses (chapter 9) - Extension of GLM-based functions (including the *network-based statistic [NBS]* and MTPC) to allow for multiple contrasts in a single function call, and to allow for both T- and F-contrasts - Permutation/randomization is now done using the *Freedman-Lane algorithm* (as in *randomise* and *PALM*), although models are limited to simple GLM's - Introduction of R's *S3 classes* to simplify plotting and summarizing results - Calculation of a network's *s-core* membership - Calculation of network *communicability* and vertex *communicability betweenness centrality* Please let me know if you have any issues, bug reports, feature requests, etc. Chris Watson

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postdoctoral fellowship at Memory Disorders Research Center, VA Boston / Boston University
by Scott Hayes 07 Feb '18

07 Feb '18

Posting for a colleague, please see description below: POSTDOCTORAL FELLOWSHIP IN THE COGNITIVE NEUROSCIENCE OF MEMORY Memory Disorders Research Center, Boston University School of Medicine and VA Boston Healthcare System The Memory Disorders Research Center (MDRC ; https://www.bu.edu/mdrc/ ) is seeking a postdoctoral fellow in the cognitive neuroscience of memory to participate in both basic and translational cognitive neuroscience studies examining the role of the medial temporal lobes in future thinking and decision-making. In addition to behavioral and neuroimaging studies in healthy subjects and individuals with selective amnesia, this position offers the opportunity to be involved in a newly funded study on prospective cognition in PTSD. The MDRC is located in a medical center with state of the art imaging facilities, and affords many opportunities for interaction with other laboratories in cognitive and clinical neuroscience. The successful applicant will have a PhD in cognitive neuroscience, psychology, or closely related field, and experience in functional neuroimaging. Interested candidates should email a CV and letter describing their research experience and interests. Please also have three letters of recommendation emailed to Dr. Mieke Verfaellie (verf(a)bu.edu) Start date is summer 2018. Scott M. Hayes, Ph.D. Associate Director Neuroimaging Research for Veterans Center Memory Disorders Research Center VA Boston Healthcare System Assistant Professor of Psychiatry Boston University School of Medicine www.bu.edu/brainlab

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thresh definition
by Ashley Cole 07 Feb '18

07 Feb '18

Dear experts, Could you please let me know what "thresh" means in funcroi-config. Like in general, sig=2, does this refer to the number of decimal points, here p<0.01? And I want the p-value less than 0.00001, does this mean that I need to assign threshold of 5? Thanks

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Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer
by Matt Glasser 06 Feb '18

06 Feb '18

I think the HCP CCF protocol is a good start: http://protocols.humanconnectome.org/ Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Colm Connolly <cconnolly(a)fsu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, February 6, 2018 at 10:41 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer Hi everybody, I¹m endeavoring to help a researcher come up with a protocol which might be ³optimal² (in some sense) for use with FreeSurfer. I¹ve not really used FreeSurfer much hence my lack of familiarity with what the recommended sequences are for use with FreeSurfer. Having searched around, I¹ve found [1]. Do the recommendations in [1] still apply? I¹d like the researcher to get good pial surface estimate so would like to be able to recommend that he perform a T2 scan as well. Having read through [2], it makes mention of T2 and FLAIR images for improving pial surface estimation. Is the FLASH image recommended in [1] appropriate for use with the -T2 or -FLAIR args to recon-all? We¹ll be running these scans on a 3T Siemens Prisma running V11c software. Are there particular scans that you recommend for this particular scanner or again does [1] apply? [1] https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&d o=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr ovepialsurfaces Thanks in advance for you time, Regards, -- Colm G. Connolly, PhD Dept of Biomedical Sciences Florida State University Tallahassee, FL 32306 Tel: +1-850-644-2105 https://www.researchgate.net/profile/Colm_Connolly2 _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Using subject specific template, atlas, & TPM
by Ramesh Babu 06 Feb '18

06 Feb '18

Dear experts, I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer. Thank you RB

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PROGRAMMER/ DATA ANALYST II
by Arpana Gupta 06 Feb '18

06 Feb '18

PROGRAMMER/ANALYST II G. OPPENHEIMER CENTER FOR NEUROBIOLOGY OF STRESS AND RESILIENCE UNIVERSITY OF CALIFORNIA, LOS ANGELES Background: The G. Oppenheimer Center for Neurobiology of Stress and Resilience (Mayer Lab) in the Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at the University of California, Los Angeles is seeking a full time Programmer/Analyst for a multi-site funded translational research group studying brain-gut microbiome interactions in obesity and functional pain disorders including irritable bowel syndrome (IBS), chronic pelvic pain and interstitial cystitis, and vulvodynia. This position will use multimodal MRI sequences to study structural and functional circuit dynamics cross sectionally and longitudinally within a dimensional systems biology approach. The programmer’s main responsibilities include: programming and optimizing automated data quality control, preprocessing, computational, and analyses pipelines for large scale multimodal brain imaging and biological data. The candidate should have a strong programming background in one or more of the following areas: bioengineering engineering, computer science, statistics, physics, and/or neuroscience. There will be opportunities to address basic and pathophysiological systems questions, in addition to work in an environment that emphasizes translational and clinical research skills (e.g. target discovery, individualized treatment development and biomarker/predictor development). The G. Oppenheimer Center of Neurobiology of Stress and resilience is a dynamic multidisciplinary group directed by Emeran A. Mayer, MD, PhD conducting clinical, translational and basic neuroscience research. You will work directly with him and an array of principle investigators, collaborators and co-investigators. Duties and Responsibilities: The Scientific Programmer and Data Analyst responsibilities will include, but are not limited to: 1. Maintain and continue to develop a full-stack application for managing and analyzing neuroimaging data <>. The back-end consists of ~9000 lines of Matlab code for processing data and over 10000 lines of MySQL stored procedures and standard SQL for triggers, views, etc. The front-end consists of ~10000 lines of Javascript/JQuery and PHP code that allows for data entry and reporting. This application is in production and stable. 2. Programming and optimizing automated data quality control, preprocessing, computational and analyses pipelines for large-scale multimodal brain imaging, including resting‐state and task-based fMRI, DTI and volumetric data. 3. Implement and support statistical analyses and scripts for biological (e.g. microbiome, genetic, etc.), behavioral, clinical and neuroscience data. This will include performing mathematical calculations/statistical analyses needed for scientific research 4. Implementation of iCloud processing and analyses pipelines such as the Human Connectome Project. 5. Implementation of data visualization programs on MRI and biological data 6. Process and analyze fMRI data: 1st level analysis 7. Work closely with data management specialist on data requests and system upgrades This would include assisting in the creation of databases, query tools for data mining, and documentation on their effective use. 8. Create and update ‘standard operating protocol’ (SOP) documents for various CNSR lab studies and/or procedures 9. Coordinate data integration from multiple ongoing studies 10. Train students and create learning tutorials for basic quality control and preprocessing of neuroimaging data. 11. Maintain detailed logs of work flow, generated codes and scripts, and documentation of processes 12. Communicate issues and concerns as they arise to PIs, nurses and other relevant research staff Required Qualifications: B.A., B.S. Masters or equivalent with background in bioengineering engineering, computer science, statistics, physics, and/or neuroscience. Quantitative and extremely proficient with multiple neuroimaging analysis platforms (HCP Pipeline, FreeSurfer, SPM, FSL, AFNI, GIFT, TrackVis, CONN, etc.). Strong programming skills and comfort with diverse computing environments required (Matlab, UNIX/BASH language, MySQL, PHP, Javascript/JQuery are essential). Strong background in statistics and statistical software scripting (e.g. R, Python, QIIME). Experience with data visualization (d3.js or other is a plus) Strong interpersonal skills and a high level of organization with careful attention to detail are absolutely required. This position requires a high degree of motivation, organization, and self‐sufficiency, although some training and supervision will be provided. Additional Qualifications: Experience with neuroimaging, biological, and behavioral databases is an advantage. Experience with network analyses, machine learning and modeling confer a significant advantage. Graphic or Web design skills are considered a plus, but not required for consideration. Additional Information: Applications must be sent by email to Dr. Arpana Gupta (AGupta(a)mednet.ucla.edu <mailto:AGupta@mednet.ucla.edu>) CCing Melenie Rosales (MRosales(a)mednet.ucla.edu <mailto:MRosales@mednet.ucla.edu>) and Cathy Liu (clliu(a)ucla.edu <mailto:clliu@ucla.edu>) Please include a CV, cover letter and names of three references. Arpana Gupta, Ph.D. Arpana Gupta, Ph.D. Assistant Professor Director, Neuroimaging Operations Core G. Oppenheimer Center for Neurobiology of Stress and Resilience Ingestive Behavior and Obesity Program Vatche and Tamar Manoukin Division of Digestive Diseases David Geffen School of Medicine UCLA CHS 42-210 10833 Le Conte Avenue Los Angeles, CA 90095-7378 http://uclacns.org/ Email: aagupta9(a)gmail.com OR AGupta(a)mednet.ucla.edu

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Freesurfer