#acl AdminGroup:read,write,delete,revert All:read = FreeSurfer Tutorial and Workshop = === Cape Town, South Africa === === 11-12 February 2010 === [[http://www.chpc.ac.za/|Centre for High Performance Computing (CHPC)]], [[http://www.chpc.ac.za/Contact/contact.php|map]] == Overview == The !FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with !FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. 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). After completing the tutorials, you should be able to: * perform surface reconstructions; * generate subcortical segmentations; * fix errors encountered during the volume or surface processing; * overlay functional data onto surfaces; * perform group analysis of structural (e.g. thickness) and functional data. Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this: ---- {{{ command arg1 arg2 }}} ---- == Question / Suggestion Box == During the course, if you have questions or suggestions, [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|please follow this link]] to submit them (anonymously, or not). We will process them during the course and give feedback at the end. == Course Evaluation == Please fill out our course evaluation [[https://spreadsheets.google.com/viewform?hl=en&formkey=dGI5U21qSU1RdDZQbE1GclNPalpsemc6MA|here]]. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave. If you started it but cannot finish it until later, enter any random 4 digit number at the top of the survey and hit submit. When you are at home, fill out a new form (skipping questions you already answered) but put that same 4 digit number in at the top so we can tie your answers together. == Course Schedule == === Thursday, February 11th - Introduction / Single Subject / Group Analysis === || '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' || || 8:00 - 8:30 || '''optional -''' [[http://www.bme.uct.ac.za/freesurfer/unix_tutorial.ppt|Unix Tutorial for FreeSurfer Users|&do=get]] [[http://www.ee.surrey.ac.uk/Teaching/Unix|1. Surrey]], [[http://docstore.mik.ua/orelly/linux/lnut/index.htm|2. O'Reilly]] || tutorial || Allison Stevens || || 8:45 - 9:00 || '''optional -''' Intro to FreeSurfer Jargon || talk || Allison Stevens || || 8:30 - 9:00 || Course Registration || sign-in || || || 9:00 - 9:30 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.intro.ppt|Introduction to Freesurfer|&do=get]]|| talk || David Salat|| || 9:30 - 10:30 || [[http://www.bme.uct.ac.za/freesurfer/fsrecon.ppt|Analyzing the Individual Subject|&do=get]] || talk|| Doug Greve|| || 10:30 - 10:45 || '''break''' || || || || 10:45 - 11:15 || Tkmedit/Tksurfer demonstration || demo || Doug Greve || || 11:15 - 11:45 || [[FsTutorial/OutputData|Interaction with Individual Subject Data Tutorial]] || tutorial || staff || || 11:45 - 12:15 || [[http://www.bme.uct.ac.za/freesurfer/mri_acquisition.ppt|MRI Acquisition Methods for Morphometry|&do=get]] || talk || Andre van der Kouwe || || 12:15 - 12:30 || '''break''' || || || || 12:30 - 13:00 || '''Working lunch''' Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain || talk || David Salat || || 13:00 - 13:30 || '''lunch''' || || || || 13:30 - 14:15 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.applications.ppt|FreeSurfer Applications|&do=get]] || talk || David Salat || || 14:15 - 14:45 || [[http://www.bme.uct.ac.za/freesurfer/fs.surface-based-analysis.ppt|Surface-based Smoothing/Surface-based Registration|&do=get]] || talk || Doug Greve || || 14:45 - 15:00 || '''break''' || || || || 15:00 - 15:45 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons|&do=get]] || talk || Doug Greve || || 15:45 - 16:00 || QDEC demonstration || demo || Doug Greve || || 16:00 - 17:00 || [[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit Tutorial]] || tutorial || staff || || 17:00 - 17:45 || [[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec Tutorial]] || tutorial || staff || === Friday, February 12th - ROIs / Troubleshooting / Multi-Modal / Q&A === || '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' || || 9:00 - 9:30 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.reliability.ppt|Accuracy, Reliability and Validation|&do=get]] || talk || David Salat || || 9:30 - 10:30 || [[http://www.bme.uct.ac.za/freesurfer/fs.roi.ppt|ROI Analysis|&do=get]] || talk || Doug Greve || || 10:30 - 11:00 || [[FsTutorial/AnatomicalROI|ROI Analysis Tutorial]] || tutorial || staff || || 11:00 - 11:30 || '''break''' || || || || 11:30 - 12:00 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.failure_modes.ppt|Failure Modes|&do=get]] || talk || Allison Stevens|| || 12:00 - 12:30 || How to QA a Recon, Troubleshooting Tutorial demonstration || demo || Allison || || 12:30 - 13:15 || '''lunch''' || || || || 13:15 - 14:15 || [[FsTutorial/TroubleshootingData|Troubleshooting Tutorial]] || tutorial || staff || || 14:15 - 15:30 || [[http://www.bme.uct.ac.za/freesurfer/fs.multimodal-integration.ppt|Multi-Modal Integration|&do=get]] || talk || Doug Greve || || 15:30 - 15:45 || '''break''' || || || || 15:45 - 16:45 || [[FsTutorial/MultiModal|Multi-Modal Integration Tutorial]] || tutorial || staff || || 16:45 - 17:30 || [[http://www.bme.uct.ac.za/freesurfer/event-related.pdf|Designing Event-related Experiments for fMRI|&do=get]] || talk || Doug Greve ||