Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 4

Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years
by Alexandru Hanganu 16 Jun '21

16 Jun '21

External Email - Use Caution Dear All, The PCAN lab: http://pcanlab.ca has a two-year funded postdoctoral research fellow position under the supervision of Dr. Oury Monchi starting immediately to work on the following project: *Neuroimaging and other predictors of cognitive and neuropsychiatric evolution in Parkinson’s disease using multi-modal MRI imaging techniques and machine learning.* The project is funded by the Canadian Institutes of Health Research (CIHR) . It involves longitudinal analyses of cortical thickness, tractography and BOLD resting-state fMRI analyses and will benefit from collaborations with Dr. Alexandru Hanganu at the Department of Psychology of the University of Montreal. Other collaborators include Dr. Nils Forkert head of the Medical Imaging Processing and Machine Learning laboratory. A special focus will be given to the neural origins and predictors of Mild Behavior Impairment (MBI) in Parkinson’s disease in collaboration with Dr. Zahinoor Ismail who has led the development of the MBI-checklist. The project will make use of an existing longitudinal study containing structural, diffusion weighted imaging and functional MRI, neuropsychological and behavioural assessment, and genotyping at three time points. The PCAN lab has been a pioneer in using different neuroimaging techniques to study the origins and evolution of cognitive more recently neuropsychiatric deficits in Parkinson’s disease with the ultimate goal of early prediction of dementia in the disease. Other interests include the function and application of neuromodulation techniques such as transcranial magnetic stimulation, Transcranial direct stimulation and low intensity focused ultrasound. The PCAN Lab is located in the Healthy Brain Aging labs of the Hotchkiss Brain Institute part the Foothills Campus of the University of Calgary. The Foothills campus is home to the Seaman Family MR Research Centre which host a General Electric 3T research dedicated MRI scanner. Requirements of the position include a PhD in Neuroscience, biomedical engineering, biomedical sciences, or Psychology with experience in the analysis of one or multiple MRI neuroimaging techniques such as cortical thickness/volumetry (e.g. *Freesurfer, FSL*), functional connectivity (e.g. *PPI, ICA, graph theory*), diffusion weighted imaging (e.g. *Dipy, MRTrix, FSL*). Some fluency in computer programming (e.g. *Linux, Unix, MATLAB, or Python)* is also required as well as the ability to write scientific peer-reviewed manuscripts. Please send applications (Cover letter, CV, and the name of 2 references including current supervisor) to Oury Monchi: oury.monchi(a)ucalgary.ca

1 1

Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

1 1

Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere
by Fraser Smith 26 Apr '21

26 Apr '21

External Email - Use Caution Hi there I have a clear parcellation error with one participant who does look to have an atypical structure around the right post-central gyrus (looks split in two). Both the pre and post central gyri are shifted significantly backwards – but only for the right not the left hemisphere. I see this has been mentioned before in the archives – but I have been unable to find a fix for this. Could you provide any tips on what to try? I am using v6.0.0. Best wishes Fraser Smith

3 3

-hires vs -conf2hires in 7.1.1.
by Alexopoulos, Dimitrios 21 Mar '21

21 Mar '21

External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

4 11

label to surface
by Sam W 02 Feb '21

02 Feb '21

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam

3 9

Post-Doctoral position available in human neuroimaging and sensory testing at the University of Minnesota School of Dentistry
by Estephan Moana Filho 13 Jan '21

13 Jan '21

External Email - Use Caution *POSITION OVERVIEW* The Division of TMD & Orofacial Pain (OFP) at the University of Minnesota School of Dentistry (UMN SOD) is seeking a highly motivated Post-Doctoral Associate in the field of human neuroimaging and sensory testing for an NIH/NIDCR funded project studying brain-related mechanisms in painful temporomandibular disorders (TMD). The focus of this position will be on acquisition and analysis of neuroimaging data, as well as performing quantitative sensory (QST) and endogenous pain modulation (EPM) testing. This project is led by Dr. Estephan J. Moana-Filho, a dentist-scientist within the TMD & OFP division, who provides clinical care to OFP patients and is interested in expanding the knowledge about brain mechanisms in OFP conditions with a focus on painful TMD. The methods to be used include multimodal magnetic resonance imaging (MRI) based on the Human Connectome Project (HCP) sequences (structural, resting and stimulus-evoked BOLD fMRI, diffusion) combined with sensory testing and psychosocial/behavioral measures (QST, EPM, questionnaires, clinical measures, etc.). Our goal is to further our understanding of brain structural and functional networks involved in sensory processing, and potentially underlying central sensitization features present in painful TMD. *Duties and Responsibilities*: The Post-Doctoral Associate’s responsibilities will include, but are not limited to: 1. Implement multimodal MRI data analysis pipelines (structural and functional connectivity, stimulus-evoked fMRI, diffusion-based tractography and volumetry/cortical thickness measures) based on the HCP pre-processing pipelines (Glasser et al., 2013). 2. Perform sensory/EPM testing in human participants following standardized protocol (Rolke et al., 2006) 3. Acquire neuroimaging data following the HCP neuroimaging approach (Glasser et al., 2016), including stimulus-evoked fMRI. 4. Model and analyze complex datasets including neuroimaging, sensory and clinical data. *Required qualifications*: 1. PhD in neuroscience, biomedical engineering, oral biology, psychology, cognitive science, or a related field. 2. Strong proficiencies with one or more major neuroimaging software suites (e.g., FSL, Freesurfer, Connectome workbench, AFNI, SPM, etc.) and Unix/Linux environment. Familiarity with R, Python, and/or Matlab programming languages is a plus*.* 3. Quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments such as high-performance computing systems. 4. Comfortable with interacting with human participants. 5. Demonstrated ability to complete projects as evidenced by first-author publication(s). 6. Proficient writing skills, motivated and driven to publish in peer-reviewed journals. In addition to these requirements, the ideal candidate should have a passion for self-learning, be inquisitive, critical problem-solving skills and initiative to seek out the resources necessary to achieve the project’s goals. The Moana-Filho lab is part of a vibrant pain research community at the UMN, with access to several resources including: · The Center of Magnetic Resonance Research (CMRR), a world class MRI research center with several research dedicated MRI scanners including three 3T Prisma, 7T and 10.5T human scanners. · The UMN Minnesota Supercomputing Institute (MSI), an interdisciplinary research resource supporting high-performance computing services. The latest MSI’s system is among the top 10 university-owned supercomputers in the nation, with a peak performance of over 670 Tflops and an additional 105 Tflops from a dedicated GPU subsystem. Its main cluster is also equipped with 40 high memory nodes to accommodate large memory requirements. These memory nodes feature 1 TB of memory and large solid state drives for ultra-high performance input/output. All systems are connected to high-performance parallel storage systems, with a current capacity of approximately 3 PBytes. MSI staff manage and operate these resources, offering full support to users in developing and optimizing workflows. Applications will be reviewed on an ongoing basis. Funding is available as a one-year appointment with the possibility of extension. Salary will be competitive and commensurate with experience. In case of any questions, please feel free to contact Dr. Moana-Filho (moana004 at umn dot edu <moana004(a)umn.edu>). To apply, click on “External Applicants” under the banner “Apply now!” and search for Job Opening 337497: https://humanresources.umn.edu/content/find-job

1 1

Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

3 5

recon-all 7.1.1
by James Hartzell 27 Nov '20

27 Nov '20

External Email - Use Caution Hi Andrew Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1. When I try to run the original patch you suggested I still get permissions problems, even with sudo. (base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer (base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin (base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup Password: (base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/reco… > recon-all zsh: permission denied: recon-all Here's hoping you can send another fix! Cheers James -- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

2 11

surface/volume editing
by Jake Jensen 27 Oct '20

27 Oct '20

External Email - Use Caution Hello, I am attempting to edit a subject, but upon removing voxels where the WM and pial surfaces should not be, the WM surface does not receed (pictures are attached). I have attempted this with -all and -autorecon2, running it again from the original 001.mgz file, as well as attempting to run it from the beginning with -clean. The end result is consistently the same, as seen in the attached images. Additionally, it is strange that the WM surface crosses the pial. I could not seem to find a solution to this in the archives. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: OSX mojave -all -autorecon2 Recon all log attached Thank you! -Jacob

2 9

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2020