Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

Talairach_afd error
by Anna I. Garcia Diaz 22 Oct '15

22 Oct '15

Dear all, I am having problems running the recon-all process. The error log is attached to this e-mail. This error appears only when I run recon-all in a machine able to parallelize preprocesses, however, if I use the same reconstructed oriented image in a machine sent as a normal job directly to the terminal, the preprocess runs without any errors and the output looks correct. I have tried to use the -notal-check flag as the error log suggests, but it fails anyway. Since our team is working in a longitudinal study, and the images from the other time points have been preprocessed with the parallelizing machine, we are concerned that using the non-parallelizing machine could add significant methodological variabilities to our studies, and we would rather be consistent with the previous procedures. Do you have any comments or further suggestions on how we might be able to fix this error? Thanks in advance for your time and help Anna Garcia

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mris_expand - problem reading thickness file?
by Alex Puckett 22 Oct '15

22 Oct '15

Hello! I'm having trouble with mris_expand using the -thickness flag. ?If I expand by a fixed distance instead of % thickness then mris_expand works no problem - the program seems to be hanging up when reading the thickness file. Has anyone else experienced this? The command I'm running (from the surf folder) is: mris_expand -thickness lh.white 0.5 lh.expandWhiteThick0p5 The output from this is: "?using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.expandWhiteThick0p5 reading thickness..." And then...nothing! Watching the CPU usage it appears that resources are used for about 10 -12 minutes and then drops to 0 and just sits there for as long as I'll let it (>4 days) - no error. Also, the thickness files do not appear to be corrupt. I can overlay the thickness data onto a surface no problem. Any help would be appreciated. Cheers, Alex --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS Linux release 7.1.1503 (Core) Kernel info: Linux 3.10.0-229.1.2.el7.x86_64 x86_64 --------------------------------------------------------------------- ?

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Sulcal depth units
by Simon Vandekar 22 Oct '15

22 Oct '15

Dear Freesurfer experts, I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. Are the units for sulcal depth in mm or are they in arbitrary units? Thanks in advance, Simon

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Postdoctoral Opportunity: Multimodal MRI registration and analysis
by Frederic Andersson 22 Oct '15

22 Oct '15

Postdoctoral Opportunity: Multimodal MRI registration and analysis Context and methodology This postdoctoral position will focus on the registration of ex-vivo onto in-vivo MR data. Based on some recent advances extending the combined volume and surface registration, efficient approaches can be provided for dealing with this issue. However, these methods need to be validated and several open theoretical questions are related to this problem and will be investigated during this postdoctoral work. The theoretical results obtained will be tested and used on real human data in a larger framework aiming at tractography validation (French National Research Agency Grant ANR 2014, collaborative study Inserm U930, Université de Tours, Neurospin and Martinos Center). Applicant profile Candidates should have a strong background in image registration and MR imaging, a good publication record, and strong experience in c++ and matlab coding. Proficiency in English is required, as well as scientific writing skills. Applicants should send a CV, including list of publications and a description of previous research experience, as well as the names and emails of two academic referees to: Clovis Tauber (clovis.tauber(a)univ-tours.fr <mailto:clovis.tauber@univ-tours.fr>) and Christophe Destrieux (christophe.destrieux(a)univtours.fr <mailto:christophe.destrieux@univtours.fr> ) Conditions Starting date: January 2016 (adjustable) Contract: 2 years Location: Imaging and Brain unit, INSERM U930, Tours. Salary: related to experience References G.M. Postelnicu, L. Zöllei, B. Fischl: Combined Volumetric and Surface Registration, IEEE Transactions on Medical Imaging 28 (4), April 2009, p. 508--522 Zemmoura I, Serres B, Andersson F, Barrantin L, Tauber C, Filipiak I, Cottier JP, Venturini G and Destrieux C 2014 FIBRASCAN: a novel method for 3D white matter tract reconstruction in MR space from cadaveric dissection Neuroimage 103 106—118 Serres B, Zemmoura I, Andersson F, Tauber C, Destrieux C and Venturini G 2013 Brain Virtual Dissection and White Matter 3D Visualization Stud. Health Technol. Inform. 184 392--396

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Research scientist/postdoctoral position in Neuroimaging
by Castillo, Gabriel 21 Oct '15

21 Oct '15

University of California San Diego and the VA San Diego Healthcare System Research scientist/postdoctoral position in Neuroimaging General Description We are seeking a highly motivated and talented researcher (either PhD or MS level) with expertise in fMRI analyses. The person in this position will conduct and coordinate research for the laboratory of Dr. Deborah Harrington at the University of California San Diego (UCSD) and the VA San Diego Healthcare System (VASDHS). The laboratory investigates changes in the brain related to cognitive and motor functioning in individuals with Parkinson’s disease and Huntington’s disease. The lab uses neuroimaging (fMRI, DTI, sMRI), behavioral, and clinical approaches to address research questions. The position provides opportunities for participation in scientific conferences and writing manuscripts/grants. San Diego has a well-established community of basic and clinical scientists who use neuroimaging methods to study healthy individuals and persons with neurological and psychiatric disorders. Neuroimaging is conducted at the UCSD Center for Functional MRI (CFMRI) (http://fmri.ucsd.edu/) which supports two research-dedicated 3T scanners. The VASDHS is adjacent to the UCSD campus (5-minute walk to CFMRI). Primary Duties and Responsibilities ● Data collection ● Analysis of neuroimaging data using AFNI, FSL, FreeSurfer or other software ● Data management ● Management of lab operations ● General research and administrative duties Necessary Qualifications ● PhD or masters in biomedical engineering, cognitive science, psychology, neuroscience, or related field ● Technical experience in fMRI and functional connectivity MRI ● Strong programming skills (e.g., shell scripting, Matlab, Python) ● Knowledge of neuroanatomy ● Strong data management skills ● Excellent organizational, interpersonal and communication (written and verbal) skills ● Prior research experience with human participants Additional Highly Desirable Skills ● Experience with data-driven techniques (e.g., ICA, graph theory) ● Strong statistical (e.g., SPSS, R) and analytical skills ● Experience in other imaging modalities (e.g., DTI, sMRI, MEG) Interested applicants should contact Dr. Deborah Harrington (dharrington(a)ucsd.edu) with a cover letter and CV. Salary will be commensurate with experience. The position will remain open until filled.

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Research Associate Position in Neuroimaging
by Castillo, Gabriel 21 Oct '15

21 Oct '15

University of California San Diego and the VA San Diego Healthcare System Research Associate Position in Neuroimaging General Description We are seeking a highly motivated individual for a Research Associate position in brain imaging and cognition. The person in this position will conduct and coordinate research for the laboratory of Dr. Deborah Harrington at the University of California San Diego (UCSD) and the VA San Diego Healthcare System (VASDHS). The laboratory investigates changes in the brain related to cognitive and motor functioning in individuals with Parkinson’s disease and Huntington’s disease. The lab uses neuroimaging (fMRI, DTI, sMRI), behavioral, and clinical approaches to address research questions. The position provides opportunities for ongoing training, meetings with collaborating scientists, and participation in scientific meetings and conferences. San Diego has a well-established community of basic and clinical scientists who use neuroimaging methods to study healthy individuals and persons with neurological and psychiatric disorders. Neuroimaging is conducted at the UCSD Center for Functional MRI (CFMRI) (http://fmri.ucsd.edu/) which supports two research-dedicated 3T scanners. The VASDHS is adjacent to the UCSD campus (5-minute walk to CFMRI). Primary Duties and Responsibilities ● Data collection (MRI, neuropsychological, behavioral) ● Analysis of neuroimaging data using AFNI, FSL, FreeSurfer or other software ● Data management ● General research and administrative duties ● Management of lab operations Necessary Qualifications ● Bachelors or masters degree in cognitive science, psychology, biomedical engineering, computer science, neuroscience, or related field ● Prior research experience with human participants ● Experience using Linux or Unix ● Strong data management skills ● Excellent organizational, interpersonal and communication (written and verbal) skills Additional Highly Desirable Skills ● Strong programming skills (e.g., shell scripting, Matlab, Python) ● Experience in neuroimaging techniques and MRI data analysis ● Experience with AFNI, FSL, or Freesurfer Interested applicants should contact Dr. Deborah Harrington (dharrington(a)ucsd.edu) with a cover letter and CV. Compensation is commensurate with skills and experience. Position will remain open until filled.

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Fwd: Comments Sought on Best Practices in Data Analysis and Sharing (COBIDAS) White Paper
by Douglas Greve 21 Oct '15

21 Oct '15

FYI -------- Forwarded Message -------- Subject: Comments Sought on Best Practices in Data Analysis and Sharing (COBIDAS) White Paper Date: Wed, 21 Oct 2015 09:32:51 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear OHBM Community, In 2014 OHBM Council created the Committee on Best Practices in Data Analysis and Sharing (COBIDAS), to identify best practices of data analysis and data sharing in the brain mapping community, prepare a white paper organizing these practices, and seek input from the OHBM community before ultimately publishing these recommendations. At long last, the COBIDAS report focused on best practices in MRI is ready for your review and input. Please visit the COBIDAS page <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3668> to view this “Proposed Final” document and provide your feedback. There you will find a link to submit your feedback, or you can send documents to info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> (please include “COBIDAS” in the subject line). Please send comments and suggested revisions by *November 17, 2015*. At that time, COBIDAS will review all feedback and begin creating the “Final” COBIDAS report. Once the final document is available, it will be posted again for the OHBM community to review and provide a Yes/No vote of your support for the report. If approved, the final document will then be submitted for publication. While many MRI guidelines have been produced over the years, this is a comprehensive and collaborative approach that is seeking input and ratification from the entire OHBM community. Your input and involvement is needed to make the final COBIDAS report a success! Read and comment on the Proposed Final draft and encourage your colleagues to do the same. Please use this COBIDAS link (http://www.humanbrainmapping.org/cobidas) when sharing via social media. Sincerely, Karl Zilles OHBM Council Chair Thomas Nichols Chair, COBIDAS *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>.

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Freesurfer 5.3 Centre of Cortical Parcellations Text File
by Nathan Malitz 21 Oct '15

21 Oct '15

Hi There, Long time listener first time caller, I would like to generate a txt file, each line with 3 values for the XYZ in normalised space, based on the centre of each free surfer cortical parcellation, for each Subject run through freesurfer. Any chance someone could point me in the right direction for this? Kind regards, Nathan

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normalization of structural volumes
by geschwind2013 20 Oct '15

20 Oct '15

Hi, FS Experts, I’m using version 5.3 and have performed hippo-subfields analysis. To perform the statistics, shall I get the normalized volumes of each hippo-subfields? or just to do correction for ICV is enough ? thanks.. Hyon

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Contrast for a group diff correlation with age
by pablo najt 20 Oct '15

20 Oct '15

Hello FS experts,I have a question about setting the following contrast in mri_glmfitMy contrast of interest:Does area.pial --age correlation, accounting for gender, differ between PT and HC? Class Female_PTClass Female_HCClass Male_PTClass Male_HCIf I set my classes are as above, should my contrast be the following: fem_PT, fem_HC, male_PT, male_HC, age1 -1 1 -1 0 ThanksPablo

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Freesurfer October 2015