Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

correlation analysis
by Raffaele Dubbioso 15 May '18

15 May '18

External Email - Use Caution Dear Freesurfer team, I'm working on correlation between fMRI data and a clinical score. Since such fMRI data correlate also with cortical thickness, I'd like to regress out this variable (cortical thickness). How can I write my fsgd file and command line mri_glmfit ? Thank you very much for your help Best regards Raffaele Dubbioso -- _______________________________________________ Raffaele Dubbioso, MD, PhD University Federico II of Naples Department of Neurosciences, Reproductive Sciences and Odontostomatology. Via Sergio Pansini, 5 80131 Napoli, ITALY phone: +39-0817464579 fax: +39-0817462667

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Neuroimaging postdoc position available at the University of Michigan
by Martijn Muller 15 May '18

15 May '18

*Research Fellow - Multimodal neuroimaging of Parkinson’s disease* A Research Fellow position is available immediately at the Functional Neuroimaging, Cognitive, and Mobility Laboratory, Department of Radiology, University of Michigan, Ann Arbor, MI, USA. Our laboratory specializes in clinical, mobility, cognition, and multimodal neuroimaging studies of Parkinson's disease and is directed by Drs. Nicolaas Bohnen, MD, PhD (Director) and Martijn Muller, PhD (Co-director). We are looking for a post-doctoral candidate to conduct and interpret multimodal and voxel-based imaging analyses of structural, functional MRI and PET datasets to address clinical research questions in patients with Parkinson’s disease. The applicant will also participate in the development of a new neuroimaging and clinical database with incorporated imaging analysis pipeline processing routines. Applicants must have completed a graduate degree (PhD) with relevant experience in multimodal imaging. The applicant must have experience in radiology/radiological sciences, signal processing, functional MRI and diffusion tensor imaging, the use of neuroimaging software packages such as SPM, Freesurfer, Matlab, and FSL. Experience in network-based methods, such as graph theory, would be highly desirable. Additional roles include leadership and active participation in project management activities including the administration of research projects, as well as some teaching sessions and supervision of students. Fluency in English conversation and team work skills to work in a multidisciplinary environment are important. This position will require self-initiative and the ability to work independently without close supervision. Send a brief letter of interest that describes how current skills fit with the required skills for this position, current curriculum vitae, names and contact information of three references to: Dr. Martijn Muller at mtmuller at umich.edu. Compensation of this limited term position will be commensurate with experience and includes health benefits. The University of Michigan is an equal opportunity/affirmative action employer. If applicable, this offer is contingent on your securing valid immigration status and work authorization before your expected start date and maintaining your valid immigration status and work authorization throughout your employment. University of Michigan Health System conducts background screening and pre-employment drug testing on job candidates upon acceptance of a contingent job offer and may use a third party administrator to conduct background screenings. Background screenings are performed in compliance with the Fair Credit Report Act.

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pcc.nii.gz vs z.nii.gz resting state
by Lauri Tuominen 15 May '18

15 May '18

External Email - Use Caution Dear freesurfers, I’m using mri_glmfit to estimate the correlation between a time series from a seed region and all the voxels in the brain. For one subject I get values in the pcc.nii.gz around .4 in my region of interest (not seed) but the z-scores are extremely high, i.e. > 4. Am I doing something totally wrong? My understanding was that z = arctanh(r). Thank you so much again! Lauri Tuominen

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Pial surface running into white surface
by Kevin Aquino 15 May '18

15 May '18

External Email - Use Caution Hi free surfer mailing list! I am having a problem with some subjects where the pial surface is running into the white surface (and terminating at some points terminating within white matter). Apologies if the solution is in the mailing list (all I could find is that this could be fixed with FS v6). The build stamp is: freesurfer-Linux-centos6_x86_64-dev-20170915- what kind of edits should I be doing? I have added the necessary files to https://github.com/KevinAquino/errorPial if you could be so kind to have a look! Cheers, *Dr Kevin Aquino* Research fellow, School of Psychology, Monash University, Australia. Hon. Research Fellow Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost

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Job offer - 2 year postdoc France
by Scott Love 15 May '18

15 May '18

External Email - Use Caution Applications are invited for a two year, full time postdoctoral position (see below for details). Contact Dr. Martine Migaud (Martine.Migaud(a)inra.fr) for questions. Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-year postdoctoral position is available in the group of Dr. Martine Migaud, at the laboratory of Reproductive and Behavioral Physiology (https://www6.val-de-loire.inra.fr/physiologie_reproduction_comportements) which brings together over 50 researchers from INRA, CNRS, the University of Tours and the French horse and riding institute (IFCE). Context and mission: The Project is part of a recently awarded grant from the French National Agency for Research and involves magnetic resonance imaging (MRI) analysis in a large animal model (sheep). This project aims to explore through MRI approaches, the mechanisms of brain plasticity in the hypothalamus, a structure involved in the control of reproduction. In this project, we aim to develop MR acquisition and post-processing methods to monitor brain changes and to obtain imaging biomarkers, based on the use of multi-modal neuro-imaging tools to investigate anatomical, connectivity and hypothalamic microstructure variations in function of the environment. Our lab makes use of sheep as an in vivo model system and for in vitro immunohistochemical and molecular approaches. The recruited post-doc will have access to the CIRE platform within the laboratory, dedicated to applied surgery and imaging of large animal models. The platform is equipped with state of the art imaging facilities including a clinical MRI scanner (3T Verio, Siemens) and a CT-Scanner (https://www6.val-de-loire.inra.fr/cire/Imagerie) He/she will also benefit from a strong collaborative local environment formed by the members of the CIRE platform and other scientists from our unit. In addition, the project is carried out in collaboration with the Team Development & Plasticity of the Neuroendocrine Brain, INSERM U1172, directed by Dr. V. Prévot. The position is available for two years and would ideally start in October 2018. Place: The laboratory is located in Nouzilly, in close proximity to Tours, in the heart of the Loire Valley, France. Tours is a pleasant city from which one can also reach Paris or Bordeaux very easily within 1h00 and 2h00 respectively by high-speed train. Candidate profile: The successful candidate will have a PhD in neuroscience, Electrical or Biomedical Engineering, or related fields with strong experience in MRI neuroimaging and in statistical analysis. Knowledge and previous experience in computer programming and analysis software (eg. Python, Matlab, C++, FSL, Freesurfer, Linux, Perl…) is mandatory. We are looking for a highly enthusiastic and autonomous candidate who can develop his/her line of research with an interest in interdisciplinary research and excellent interaction and communication skills in the context of a collaborative teamwork. To apply, please send by e-mail, your C.V., a motivation letter and the names and contact information of two referees to Dr. Martine Migaud (Martine.Migaud(a)inra.fr) We will consider applications until August 31, 2018.

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macOS Sierra installation error
by NR K 14 May '18

14 May '18

External Email - Use Caution Hello FreeSurfer Developers, My name is Narae. I'm attempting to install Freesurfer on MacOS Sierra 10.12.6. I already followed step-by-step manual on the freesurfer wiki. I installed XQuartz 10.11 and complete the installing process. But there was nothing to change on Terminal and the command for set the location Freesurfer installed. When I entered command down below, terminal said 'export: command not found' $> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh To solve this, I followed some clips on youtube but it didn't work, too. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? I hope I can solve this and use your awesome tools soon. Please help me, Thank you in advance! 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwi…> 2) Platform: MacOS Sierra 10.12.6)

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Reminder to Register for HCP Course 2018
by Jennifer Elam 14 May '18

14 May '18

External Email - Use Caution Only a few weeks until the *2018 HCP Course: "Exploring the Human Connectome"*! For more info and to register visit the HCP Course 2018 website <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…> . A limited number of registrations with accommodation at Worcester College included are available until filled, or May 29 at the latest. FreeSurfer is a major part of the HCP structural processing pipeline used for the released HCP Young Adult data, and continues to be used in the processing of forthcoming Lifespan HCP data. HCP Course 2018 will be held June 25 – 29 at the Blavatnik School of Government <https://www.bsg.ox.ac.uk/partner/contact-us>, at the University of Oxford <http://www.ox.ac.uk/>, in Oxford, UK. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis. The course is also a great way to get up to speed on HCP tools including Connectome Workbench <https://www.humanconnectome.org/software/connectome-workbench> (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA <https://balsa.wustl.edu/> database. If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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volume to surface registration
by Wang, Zhuonan 14 May '18

14 May '18

Hi Team, I have a functional image which located in the FSL volume-based template(MNI152), and now I wanna to register this image to FS-based surface template (MNI305). How can I do this? Please let me know how to do this! PS: I'm not sure that the MNI152 is same as the FS's MNI152. Dataset File: MNI152_T1_1mm_brain.nii Identifier Code: NII_MkcC7NBmrrzYGzBC6bOpTA Creation Date: Thu May 10 13:01:49 2018 Template Space: MNI Dataset Type: Anat Bucket (-abuc) Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST] Storage Mode: NIFTI Storage Space: 14,442,064 (14 million [mega]) bytes Geometry String: "MATRIX(1,0,0,-90,0,-1,0,126,0,0,1,-72):182,218,182" Data Axes Tilt: Plumb Data Axes Orientation: first (x) = Right-to-Left second (y) = Posterior-to-Anterior third (z) = Inferior-to-Superior [-orient RPI] R-to-L extent: -90.000 [R] -to- 91.000 [L] -step- 1.000 mm [182 voxels] A-to-P extent: -91.000 [A] -to- 126.000 [P] -step- 1.000 mm [218 voxels] I-to-S extent: -72.000 [I] -to- 109.000 [S] -step- 1.000 mm [182 voxels] Thank you! Zhuonan

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Extract time-courses by ROI from preproc-sess preprocessed data
by Ben Smith 14 May '18

14 May '18

External Email - Use Caution I have an event-related paradigm with variable length, and I would like to get a functional activity parcellation ROI measurement for each trial individually in order to enter into a reinforcement learning model at a trial level. Can I extract ROIs for parcellations directly from preprocessing output (e.g., fmcpr.sm5.fsaverage.rh.nii.gz) created by preproc-sess? I would then apply an HRF gamma function myself to each time series and then match each trial to the activity at that time point. I initially tried creating paradigm files for mkanalysis-sess where every trial was essentially its own condition. But this seems clumsy and might not work well because there's a differing number of 'conditions' (trials) in different subjects and runs. So now I'm wondering if there's a way to extract time courses associated with each cortical parcellation? So, for instance with the Destrieux Atlas there are 58 parcellation units, so for each session I would be ultimately looking for a 58**t* matrix where *t* is the number of time points in that session. I've already run the anatomical parcellations, so I'd think the next step is to match those to the preprocessed functional data like fmcpr.sm5.fsaverage.rh.nii.gz, then extract across the time course. I tried: mri_segstats \ --seg functional_preprocessed/sub261sess/bold/004/fmcpr.sm5.fsaverage.rh.nii.gz \ --annot $SUBJECTS_DIR/msm20171025T154741sub261/label/rh.aparc.annot \ --avgwf testoutavgwf.dat --sum testoutsum.dat This ran, but didn't create testoutavgwf.dat in the working directory, though I did get a testoutsum.dat. But the time course is what I'm looking for in this case. Is it possible to do what I'm doing or should I be inputing a result from vol2surf instead of from preprocessing output? Thanks in advance for any help you can provide! Best regards Ben Smith

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ASEG Extraction Inquiry
by David S Lee 14 May '18

14 May '18

External Email - Use Caution Hi FreeSurfer Experts, I have extracted ASEG volumes using "asegstats2table" and have a few questions about the output. 1. I get values of "0" for Left and Right "WM-hypointensities" as well as "non-WM-hypointensities". Does the ASEG segmentation for WM-hypointensities only produce whole brain measures (Left and Right combined) ? 2. Most measures are separated by Left and Right, but some are not. So, are these values pertinent to both hemispheres (whole brain?) 3. Is there a reference page I can check to see what each of the measures mean (i.e. atlas)? Thank you for your time! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Freesurfer May 2018