Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

convert label to mgh
by Yang, Daniel 09 Nov '15

09 Nov '15

Dear FreeSurfer Experts, Is it possible to convert a label file to a surface-based mgh file? Could you please provide an example (e.g., on a white surface)? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

2 2

Research Scientist job in fMRI data analysis
by Pablo Velasco 09 Nov '15

09 Nov '15

New York University is looking for an Assistant Research Scientist who will work with faculty in the Center for Brain Imaging (CBI) to help implement analysis techniques, establish data analysis streams, and to make state-of-the-art MR techniques such as multi-echo/multi-plexed BOLD fMRI, diffusion imaging, and advanced anatomical measurements available to the broader research community. Responsibilities include: - Assisting in training graduate students, postdocs, and new researchers in neuroimaging data collection and analysis, including use of FSL, SPM, Freesurfer, AFNI and Matlab-based toolboxes. - Consulting with researchers to select appropriate tools and methods for data analysis, including modern statistical techniques for multiple-comparisons correction, denoising, multivariate analyses, functional connectivity analyses, and surface-based analyses. - Technical support and training for faculty, staff, and students acquiring MRI data, primarily on Siemens Prisma scanner. - Organizing training workshops and seminars to expose researchers to new developments in imaging methods and analysis techniques. - Expertise in EEG and TMS a plus. Qualified applicants should have: - A PhD or equivalent experience in Psychology, Neuroscience, Mathematics, or Statistics. - Two years relevant experience or equivalent combination, which must include experience with MR imaging principles, research training, data acquisition and analysis, statistics, and/or signal processing. - Excellent interpersonal, organizational and writing skills. - Ability to effectively communicate with individuals of all levels. - Strong analytical skills. - Ability to multitask and work independently. Salary to be commensurate with experience. Interested individuals should contact Pablo Velasco, Ph.D. at pablo dot velasco at nyu dot edu New York University is an Equal Opportunity Employer. New York University is committed to a policy of equal treatment and opportunity in every aspect of its hiring and promotion process without regard to race, color, creed, religion, sex, pregnancy or childbirth (or related medical condition), sexual orientation, partnership status, gender and/or gender identity or expression, marital or parental status, national origin, ethnicity, alienage or citizenship status, veteran or military status, age, disability, predisposing genetic characteristics, domestic violence victim status, unemployment status, or any other legally protected basis. Women, racial and ethnic minorities, persons of minority sexual orientation or gender identity, individuals with disabilities, and veterans are encouraged to apply for vacant positions at all levels.

1 0

How to compute area of subcortical structures
by anirudh nihalani 09 Nov '15

09 Nov '15

Hi, I am trying to find how to compute the area of subcortical structures like amygdala, hippocampus, thalamus etc. I have checked stats/aseg.stats file but it doesn't have areas. I looked at mri_asegstats and mris_anatomicalstats commands. Using mris_anatomicalstats I am able to compute surface area of cortical structures. But I am unable to figure out how to compute area of subcortical structures. Please suggest or give some pointers on how to achieve this. Thank you. Regards, Anirudh

2 1

recon-all error message
by Nicole Zurcher 09 Nov '15

09 Nov '15

Dear all, One of my freesurfer recons is failing and I am not sure how to troubleshoot. This is the error message that I get at the end of the recon-all log file: mris_calc -o lh.area.mid lh.area add lh.area.pial WARNING: # of slices=-106 in header - assuming 124... read_signa([path]/surf/I.001): could not open file No such file or directory mris_calc: could not establish read access to 'lh.area'. No such file or directory and this is the command that appears in the recon-all.error CMD mris_calc -o lh.area.mid lh.area add lh.area.pial See attachment for entire recon-all log file. Any help is greatly appreciated. Thanks a lot Nicole

2 1

can't change common-space subject in qdec
by Hubbard, Catherine 09 Nov '15

09 Nov '15

Dear Freesurfers: I've encountered the same problem as posted previously by Laura some time ago (see below), I am using qdec 1.5 with freesurfer version 5.3. freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Basically, I cannot change the common-space subject from the default fsaverage to my own custom template, which I have been able to do easily in the past. I should mention that we have recently made some changes to our server, so I'm not sure if this is related but suspect it is - I am also running Java8 also we are running ubuntu and here are some of the details regarding the environment I'm working in: CPU: 12-core Xeon E5 at 2.7 GHz GPU: 2 Radeon HD 7900 RAM: 64 GB (4x16 GB) of 1866 MHz DDR3 ECC Storage: 1 TB PCI-e Flash OS: Ubuntu Server 14.04.3 LTS Desktop Environment: Gnome 3.9.90 Java SE Runtime Environment: build 1.8.0_66-b17 GCC: 4.8.4 MATLAB: R2015a (8.5.0.197613) Freesurfer installation: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 tcsh version: 6.18.01 (Astron) libjpeg62-dev: installed Thanks for all your help!

1 0

Re: [Freesurfer] Issues with fsgd g2v1
by Martin Reuter 09 Nov '15

09 Nov '15

Dear Heidi, 1. you need to specify --surface <subj> <hemi> for your data, subj is where the surface stack was created, usually fsaverage, and hemi is lh in your case (base on your input name for y). 2. you need to source freesurfer. The license file needs to be in FREESURFER_HOME (a file called .license). There should be lot's of comments in the archive of this mailing list about that. Best, Martin On 11/09/2015 04:49 AM, Heidi Foo wrote: > Dear Martin, > > I was trying out the mri_glmfit command. However, I have encountered > some problems with it and I was hoping that you could help me with it. > > When inputing the --y input file, it showed an error to use '--surface > subject hemi' with surface data (Attached the file). > > Also, when using tksurfer/tkmedit commands, an error that the > freesurfer license is not found. > > Would you kindly advice me on what I should do? > > Any help is very much appreciated. > > Thanks! > > Regards, > Heidi Foo -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

1 0

extract pial surface
by Sandy Schramm 09 Nov '15

09 Nov '15

Dear experts, how can I extract pial surface (in mm2) of all our participants? Performing aparcstats2table -meas area extracts white area. Thanks, Sandy

3 3

Curvilinear interaction with age
by Yang, Daniel 08 Nov '15

08 Nov '15

Dear FreeSurfer experts, I have a group variable (X) with two levels and I want to test if there is a curvilinear interaction with age (Z). Can this be tested in FreeSurfer? Specifically, the model would be Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error I want to test b5 while controlling for b0-b4. Many thanks! Daniel

2 2

cannot start freesurfer from terminal
by André Schmidt 08 Nov '15

08 Nov '15

Dear FS experts, Surprisingly, I am no longer able to start freesurfer from the terminal: Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Do you know what I am doing wrong? Thank you Andre

2 2

Postdoctoral Position in Neuroimaging – Quantitative Neuroimaging Laboratory (QNL), Cognitive Neuroscience Division, Columbia University, NYC
by Ray Razlighi 06 Nov '15

06 Nov '15

Postdoctoral Position in Neuroimaging – Quantitative Neuroimaging Laboratory (QNL), Cognitive Neuroscience Division, Columbia University, NYC *Job Summary:* QNL invites applications for a full-time postdoctoral position to conduct processing and analyzing of PET and MRI neuroimaging data, as part of multiple research studies on aging and Alzheimer’s disease. *Principal Responsibilities:* The primary responsibility of this position includes developing novel image processing and statistical analysis methods for reconstruction of brain Beta Amyloid PET images and its accompanying structural MRI and fMRI data from healthy and diseased participants of multiple studies all focusing on aging and Alzheimer’s disease. The QNL is a new research infrastructure housed in the Cognitive Neuroscience Division of the Columbia University Medical Center Neurology Department. The main focus of the QNL is to develop techniques to quantify structural and functional brain images which allow researchers and clinicians to detect brain-based effects that are normally beyond the sensitivity and specificity of commonly-used detection methods in the field. We aim to achieve this goal by utilizing state-of-the-art signal and image processing tools as well as mathematical and statistical method. We are affiliated with Columbia’s Biomedical Engineering Department, Sergevsky Center, and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain. *Required Qualifications:* · PhD in Biomedical/Electrical Engineering, Computer Science, Medical Physics, Neuroscience or related disciplines. · Strong background in MRI analysis and related statistical methods for research (SPM, Freesurfer, FSL, AFNI or similar). · Experience with image processing and data analysis. · Strong computer programming skills (e.g., in C/C++, Matlab, R, and especially Python) are highly desirable. · Ability to think independently and work collaboratively. *Benefits* · Columbia University officers' benefits applies · Starting date: Jan 2015. · The postdoctoral position is scheduled initially for two years (open to renewal). · Salary will depend on experience. *Additional Information:* To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically at: academicjobs.columbia.edu/applicants/Central?quickFind=61752 Ray Razlighi Assistant Professor in Neurology Adjunct Assistant Professor in Biomedical Engineering Email: qr2108(a)cumc.columbia.edu

1 0

← Newer
1
...
15
16
17
18
19
20
21
...
24
Older →

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 November 2015