FREESURFER TUTORIAL PDF

We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link this link during the course presents excessive and unnecessary load on our network, and likely will fail due to this load. Please contact a staff member for help in getting this data if needed outside of the course. The talks and tutorials should familiarize you with FreeSurfer's volume and surface processing streams.

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We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link this link during the course presents excessive and unnecessary load on our network, and likely will fail due to this load.

Please contact a staff member for help in getting this data if needed outside of the course. The talks and tutorials should familiarize you with FreeSurfer's volume and surface processing streams. The tutorials also describe some of FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer overlaying color-coded parametric maps onto the cortical surface and visualizing plotted results.

Note: During the tutorial sessions, you will be shown a variety of commands. Only those that appear in a box should be copy-and-pasted into the terminal. For a list of equivalent keyboard commands on a Mac, please refer to MacCommands. Online Question Forum Videos of Lectures Throughout the course, you may post questions here anonymously or not.

You can find videos of the lectures here. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream. Research backgrounds of past and present staff members can be found on the LCN website. Purchase our awesome FreeSurfer T-shirts here.

Additional Useful Information During the Course Getting the tutorial data necessary only if you are not taking a formal course where data is provided DO NOT attempt this during a course! Contact a staff member for instructions on how to get this data locally during the course.

Download gedit, here. Some basic information on text editors can be found here. Getting the tutorial data. Throughout the course, you may post questions here anonymously or not. Introduction to Freesurfer. Analyzing the Individual Subject. Freeview demonstration. Introduction to FreeSurfer Output. Lunch Suggestions for where to eat. ROI Analysis. Group Analysis. FreeSurfer Troubleshooting. Troubleshooting Tutorial.

Quality Checking a Recon. Multiple Comparisons. Multiple Comparisons Tutorial. Longitudinal FreeSurfer. Multi-Modal Integration, Part 1: Registration. Multi-Modal Integration Tutorial, Part 1. Introduction to Diffusion MRI. Basics of fMRI Analysis. Resting State fMRI.

Multi-Modal Integration Tutorial, Part 2.

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Martinos Center for Biomedical Imaging used for a number of procedures including: Creation of computerized models of the brain from magnetic resonance imaging MRI data. Processing of functional magnetic resonance imaging fMRI data. Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes. Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions.

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FreeSurfer Tutorials

It also registers the individual cortex surfaces to surface-based anatomical atlases Desikan-Killiany, Destrieux, Brodmann. The process is fully automatic and the results can be imported in Brainstorm with just a few mouse clicks. Important note : Whether you are using FreeSurfer for the T1 segmentation, the cortical atlases or the FSAverage subject default: please register on their website registration page and cite the appropriate references. It just takes some time because the distribution package is huge get ready to download several Gb. You have two options: you have a Linux system and you want to install FreeSurfer, or you don't and you want to run FreeSurfer in a Linux virtual machine. The process is fully automatic, but quite resource-consuming. Everything is ready to be imported in Brainstorm.

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