Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30058 discussions

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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Research technician opening at Wash U Neurology
by Yendiki, Anastasia 26 Jan '18

26 Jan '18

RESEARCH TECHNICIAN POSITION IN NEUROIMAGING POSITION SUMMARY: Applications are invited for a research technician at Washington University in St. Louis. This well-established laboratory studies the structural and functional organization of the human brain using multi-modal imaging: including magnetic resonance imaging (MRI) and positron emission tomography (PET). The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Benefits of this position include: 1) Involvement in cutting edge research performed by a leading neuroimaging research laboratory 2) Potential to be involved as an author on manuscripts 3) Potential to present results at national and international conferences 4) Ability to attend talks and lectures in the field. Funding is guaranteed for up to 2 years. PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the research technician will be to archive/organize images (large multi-modal imaging datasets) and process neuroimaging data. The technician will study how disease affects the human brain by integrating large multi-modal imaging datasets and analyzing the relationship between brain imaging markers and clinical status. The technician will assist in various lab maintenance, transfer of files, database management, and organizational duties including tracking project progress, meet grant deadlines, and anticipate project needs. Qualifications: The qualified candidate should have at least a Bachelor's degree in human biology, neurosciences, psychology, bioengineering, computer sciences, or other related fields. The qualified candidate must have computer skills and knowledge of computer languages (e.g. Matlab, Python, shell scripting in CSH or BASH). The research technician must be dependable, have good attention to details, be well organized, be self-motivated, and be comfortable working as part of a team environment. Previous experience with neuroimaging data analysis programs is preferred but not required. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110

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Re: [Freesurfer] Hippocampus Subfield analysis error
by Shan Hannah Luo 26 Jan '18

26 Jan '18

Hi Andrew, thanks for your reply. Yes, I am using bash and my operating system is Mac OS X 10.9.5. Could you direct me how to set a path correctly? I ran recon_all fine. On Wed, Jan 24, 2018 at 1:14 PM, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: > Hi Hannah, > > > > What kind of environment are you running this in? These errors make it > seem like you do not have a PATH variable set at all. Are you using bash? > and what operating system? > > > > best > > Andrew > > > > > > > On Jan 22, 2018, at 4:06 AM, Iglesias Gonzalez, Eugenio < > e.iglesias(a)ucl.ac.uk> wrote: > > > > > > Hi Hannah, > > > This seems like a more general problem with your PATH, but I’m sure > Andrew (CCed) has a better idea of what might be going on. > > > Cheers, > > > /Eugenio > > > > > > -- > > > Juan Eugenio Iglesias > > > ERC Senior Research Fellow > > > Translational Imaging Group > > > University College London > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > jeiglesias.com&d=DwIGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r= > KJthMqWw4OBi4XmtFDLHhQ&m=ZaKfBrAuyRsXIKre92fMvvPb77h_SvySEbgBUJOgLiM&s= > h744EAFP3ZR0HURi0cl4du0JQime2YET6lIh-INZJcs&e= > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__cmictig. > cs.ucl.ac.uk_&d=DwIGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r= > KJthMqWw4OBi4XmtFDLHhQ&m=ZaKfBrAuyRsXIKre92fMvvPb77h_SvySEbgBUJOgLiM&s= > ovG8neKhH3sGEwGqRi5OeKX-E4aLdh0zeuZYBniwaG0&e= > > > > > > > > > On 20/01/2018, 00:23, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf > of Hannah's USC Email" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf > of shanluo(a)usc.edu> wrote: > > > > > > > > > Hi Freesurfer experts, > > > > > > I tried to do hippocampus subfield analysis but failed. I got this > error message: > > > > > > #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 > 15:27:36 PST 2018 > > > dirname: Command not found. > > > pwd: Command not found. > > > pwd: Command not found. > > > /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. > > > #-------------------------------------------- > > > #@# Hippocampal Subfields processing (T1 only) right Fri Jan 19 > 15:27:36 PST 2018 > > > dirname: Command not found. > > > pwd: Command not found. > > > pwd: Command not found. > > > /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. > > > > > > Your help would be greatly appreciated. Thanks! > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. > nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c= > clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=KJthMqWw4OBi4XmtFDLHhQ&m= > ZaKfBrAuyRsXIKre92fMvvPb77h_SvySEbgBUJOgLiM&s=nAlemdWlQJCLxi_63U- > PEBEjbULXp2FaLQA0GUgzi6Q&e= > > > > > > > > > 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 > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > partners.org_complianceline&d=DwIGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN > 0H8p7CSfnc_gI&r=KJthMqWw4OBi4XmtFDLHhQ&m=ZaKfBrAuyRsXIKre92fMvvPb77h_ > SvySEbgBUJOgLiM&s=-EJZERU1tZAo0E9Ma0DrkvnV70qUsZwJPStubsuwxEU&e= . 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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gtmpvc output stat result in negative uptake value
by Chakmeedaj Sethanandha 26 Jan '18

26 Jan '18

Dear Freesurfer experts, We found that a stat file in gtmpvc output folder shows that one area has negative avg uptake value. What could explain this result? Quoted the row from the file: 11 26 Left-Accumbens-area subcort_gm 3 2.351 -0.490 2.3033 The command used is as in the log file. Best regards, Jak

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PetSurfer: Other quantification algorithms?
by Elijah Mak 25 Jan '18

25 Jan '18

Dear Doug, In addition to the MRTM approaches, I was wondering if you have any plans to implement other algorithms in PetSurfer, such as supervised cluster analysis for extracting reference tissue activity? I am working with [11C]PK11195 PET data (neuroinflammation), for which there is no suitable reference region in neurodegenerative conditions. Hope to get your take on this please. Thanks very much. Best Wishes, Elijah

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