Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Strange Segmentation
by Maksimovskiy, Arkadiy 29 Jan '18

29 Jan '18

Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School [cid:image001.png@01D39915.A264E300][cid:image002.png@01D39915.A264E300][cid:image003.png@01D39915.A264E300][cid:image004.png@01D39915.A264E300][cid:image005.png@01D39915.A264E300]

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To Yendiki, Anastasia on TRACULA
by Renew Andrade 29 Jan '18

29 Jan '18

Dear Anastasia: All the output I get is the if Expression Syntax.

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strange output from lme analysis - Max r value=inf
by Valsasina Paola 29 Jan '18

29 Jan '18

Dear all I am using the lme toolbox to perform a longitudinal comparison of cortical thickness among 4 patient groups. Following the lme tutorial, I concatenated all files and I built a design matrix with following columns: -one column for intercept (all ones) -one column for time -four columns for each group (1 for subjects belonging to the group, zero otherwise) -four columns for group by time interaction I then built appropriate contrasts to test the effects of time, group and time x group effect; e.g., to test time x group interaction between group 1 and group 2, I built the following contrast: CM.C=[0 0 0 0 0 0 1 -1 0 0] However, I obtain quite strange results, because I get a lot of very small, very significant clusters of difference (having max t value = inf or -inf). Do you have any idea of the reason why I am getting this strange output? In your opinion, is there anything wrong in my design matrix or in the way I defined the contrasts? This is the first time I am trying to compare four groups in the same LME models, I previously ran LME statistics including just one or two groups, and everything ran smoothly. Please see a snapshot of my output statistic below: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 -inf 112586 0.96 -19.0 -95.2 8.3 1 lateraloccipital 2 -inf 93693 0.89 -22.0 54.4 16.4 1 rostralmiddlefrontal 3 inf 29207 0.86 -35.9 46.6 -9.9 1 parsorbitalis 4 inf 158564 0.78 -13.7 -98.8 2.3 1 lateraloccipital 5 -inf 67614 0.69 -8.3 35.1 25.4 1 superiorfrontal 6 -inf 123144 0.69 -40.3 19.5 29.8 1 caudalmiddlefrontal 7 -inf 2273 0.68 -55.6 -30.9 24.2 1 supramarginal 8 -inf 140663 0.67 -6.2 39.1 -4.4 1 rostralanteriorcingulate 9 -inf 5857 0.64 -35.5 8.6 50.8 1 caudalmiddlefrontal 10 inf 87756 0.61 -14.1 -98.2 1.7 1 lateraloccipital 11 inf 95576 0.56 -43.9 24.5 27.5 1 rostralmiddlefrontal 12 -inf 112122 0.56 -29.0 -62.8 35.9 1 inferiorparietal 13 inf 54800 0.54 -18.7 -59.3 2.6 1 lingual 14 -inf 140378 0.53 -19.0 -42.5 62.6 1 superiorparietal 15 inf 99044 0.49 -43.7 -20.0 52.6 1 postcentral 16 inf 119372 0.47 -52.1 -2.5 25.5 1 precentral 17 -inf 125951 0.47 -44.3 -55.1 12.7 1 inferiorparietal 18 inf 8776 0.46 -57.0 -2.0 11.7 1 precentral 19 inf 10137 0.44 -27.8 -49.8 -1.9 1 lingual 20 inf 20153 0.42 -6.6 13.8 29.5 1 caudalanteriorcingulate 21 -inf 19380 0.40 -61.6 -8.6 13.7 1 postcentral 22 -inf 38802 0.39 -23.9 -56.1 49.0 1 superiorparietal 23 inf 53936 0.38 -45.3 -25.9 46.7 1 postcentral 24 inf 45406 0.35 -38.8 -36.8 36.7 1 supramarginal 25 -inf 46213 0.32 -6.4 -47.6 15.7 1 isthmuscingulate 26 inf 41829 0.26 -61.1 -8.7 10.5 1 postcentral 27 -13.032 76609 0.40 -14.4 -15.8 64.7 1 precentral 28 12.272 78924 0.27 -6.0 -6.5 30.3 1 posteriorcingulate 29 -10.960 822 0.63 -51.8 -30.1 -17.2 1 inferiortemporal 30 10.326 96572 0.48 -31.7 11.6 0.5 1 insula 31 -8.509 43473 0.54 -62.2 -26.3 6.7 1 superiortemporal .. continued with a lot of significant clusters, all 1 vertex in size .. Thank you for any suggestion Best regards Paola Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail.

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Neurohackademy: summer school in neuroimaging and data science, July 30th - August 10th, 2018
by Ariel Rokem 29 Jan '18

29 Jan '18

We are happy to announce a call for applications to participate in Neurohackademy 2018! This two-week hands-on workshop (formerly "Neurohackweek"), held at the University of Washington eScience Institute in Seattle, July 30th - August 10th, 2018, will focus on technologies used to analyze human neuroscience data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, OpenfMRI, etc.), and on tools for making human neuroscience research open and reproducible. Neurohackademy sessions in the first week will include lectures and tutorials on data science, machine learning, data visualization and data resources. The second week will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. Instructors include Deanna Barch, Eva Dyer, Fernando Perez, Russ Poldrack, Jake Vanderplas, Gael Varoquaux, Tor Wager, and Kirstie Whitaker, among others. *For more details, see: https://neurohackademy.github.io/ <https://neurohackademy.github.io/>* We are now accepting applications to participate from trainees and researchers in different stages of their career (graduate students, postdocs, faculty, and research staff) at: https://form.jotform.com/80126067304145 Ideally, applicants should have some prior experience with neuroscience data analysis, but we welcome applications from participants with a variety of relevant backgrounds. Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (see application form for details). *Important dates:* *March 19th: Application deadline* *April 5th: Notification of acceptance* *April 23rd: Final registration deadline* On behalf of the instructors, Ariel Rokem, University of Washington Tal Yarkoni, University of Texas, Austin

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TRACULA path segmentation fault error because of bedpostx?
by Carissa Nicole Weis 28 Jan '18

28 Jan '18

Hello all, I've been running trac-all from the command line without the configuration file since I'm not changing any defaults. I've successfully run several subjects through the trac-all -prep stage, and the -bedp stage. **Although I never got the "trac-all -bedp finished without error" prompt in the -bedp terminal output and usually just get something that says at the end: ../freesurfer_6.0/bin/bedpost_mgh: line 440: 46773 Terminated ${subjdir}.bedpostX/monitor OR it'll make it to something like... 37 slices processed 38 slices processed Queuing post processing stage 46 slices processed ...and that's as far as the output in the terminal goes. It appears all the expected files have been created in dmri.bedpostx/ so I was assuming this step had been completed. However, when I go to run the -paths step I get an error that says: Loading DWIs from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/dmri/dwi.nii.gz Loading mask from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri.bedpostX Loading b-values from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals Loading gradients from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvecs INFO: Found 3 baseline images (b = 0) out of a total of 38 frames Segmentation fault Linux compute-026.mortimer 2.6.32-696.18.7.e16.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Tue Jan 9 09:34:58 CST 2018 I've checked the mask and it looks fine. I can't imagine the bvals and bvecs files should be the issue since I already made it through the -prep stage. Is it something with my bedpost outputs?? Thanks for your help! Carissa

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tracula flags
by Renew Andrade 28 Jan '18

28 Jan '18

Hello everyone! I have this problem with TRACULA. When I go to the second part of the tutorial I can´t keep going. I acknowledge that during the first part I have switch from tcsh to bash depending on errors but I’m not sure if that is normal or a mistake. The error is for example: trac-all -prep -c home/andraderenew/Downloads/freesurfer data tutorial/diffusion_tutorial/dmrirc.tutorial if: Expression Syntax Thanks!

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Postdoctoral positions in machine learning
by Walter Hugo Lopez Pinaya 27 Jan '18

27 Jan '18

Dear colleagues, We are looking for two Postdoctoral Research Associates with a background in electrical engineering, physics, statistics or computer science to work on a research project involving the application of machine learning methods to structural Magnetic Resonance Imaging data. The project is a collaboration between King’s College London, UK (Dr. Andrea Mechelli), the University of New Mexico, USA (Prof. Vince Calhoun) and the Universidade Federal do ABC, Brazil (Prof João Sato). The post holders will be based at the Institute of Psychiatry, Psychology & Neuroscience (King’s College London). For more information, please go to: https://www.hirewire.co.uk/HE/1061247/MS_JobDetails.aspx?JobID=78521 I would be happy to answer any queries from prospective applicants. Kind regards, Walter Pinaya

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Hippocampal and amygdala analysis with dev6 FS
by Erik O'Hanlon 26 Jan '18

26 Jan '18

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Scientific Programmer/ Data Analyst II
by Arpana Gupta 26 Jan '18

26 Jan '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. 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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image analyst position in NYC
by Bruce Fischl 26 Jan '18

26 Jan '18

FYI ---------- Forwarded message ---------- Date: Fri, 26 Jan 2018 19:58:00 +0000 From: "Brickman, Adam M." <amb2139(a)cumc.columbia.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, "salat(a)nmr.mgh.harvard.edu" <salat(a)nmr.mgh.harvard.edu> Subject: position in my lab Dear David and Bruce, I have an open position in my lab for a senior (master’s level-ish) image analyst, which I’m having trouble filling. I was hoping you guys might know of someone who is either looking in NY, already moving to NY, or interested in moving to NY. I’m pasting the link to the position below. Many thanks and best regards, Adam Brickman jobs.columbia.edu/applicants/Central?quickFind=165135

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