Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline

Hello Doug, Thanks for the patience. Here's the output from the terminal when I ran mri_glmfit. Best, Paul /Applications/freesurfer START: LONGITUDINAL CORTICAL THICKNESS 1000 1000_1 1000_1.long.1000 1000_2 1000_2.long.1000 1001 1001_1 1001_1.long.1001 1001_2 1001_2.long.1001 1003

[Freesurfer] Hippocampal and amygdala analysis with dev6 FS

Hi FS experts, I've been running into numerous issues trying to run the new amygdala and hippocampal analysis. I processed my data with v6.0 and obtained the 12 subfield measures with the v6.0. I have tried to add the new amygdala and subfield measures from the dev verion but am now getting

[Freesurfer] Misalignment between functional and anatomical data with bbregister

Dear Freesurfer Team, I am an image processing novice and am trying to register resting-state data to an anatomical scan using bbregister. The T1s have been run through Freesurfer's reconall pipeline, and the EPIs have undergone the following preprocessing steps: - slice time correctoin -

[Freesurfer] Scientific Programmer/ Data Analyst II

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

[Freesurfer] image analyst position in NYC

FYI -- Forwarded message -- Date: Fri, 26 Jan 2018 19:58:00 + From: "Brickman, Adam M." To: Bruce Fischl , "sa...@nmr.mgh.harvard.edu" Subject: position in my lab Dear David and Bruce,

[Freesurfer] Research technician opening at Wash U Neurology

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

Re: [Freesurfer] Hippocampus Subfield analysis error

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 wrote: > Hi Hannah, > > > > What kind of environment

Re: [Freesurfer] gtmpvc output stat result in negative uptake value

The GTM is just a general linear model, so there are no constraints on sign. The GTM makes some assumptions about the nature and magnitude of the PVEs (linear, gaussian, with the FWHM that you supply). Violations of these assumptions can cause negative values. There are a lot of other things