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| = FreeSurfer Tutorial = | [[FreeSurferWiki|top]] |
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| [wiki:Self:FsTutorial/Overview 1. Tutorial Overview] [[BR]] [wiki:Self:FsTutorial/InstallAndSetup 2. Installation and Setup] [[BR]] [wiki:Self:FsTutorial/MorphAndRecon 3. Morphometry and Reconstruction] [[BR]] [wiki:Self:FsTutorial/GroupAnalysis 4. Group Analysis] [[BR]] [wiki:Self:FsTutorial/Visualization 5. Visualization and Inspection of Group Analysis Results] [[BR]] [wiki:Self:FsTutorial/FSLFeatFreeSurfer 6. Applying FreeSurfer Tools to FSL fMRI Analysis (FEAT)] [[BR]] |
= FreeSurfer Tutorial and Workshop = ##||||'''Course Policies'''|| ##||'''Laptop damage policy''' || '''Getting the tutorial data''' || ##||If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!|| Please DO NOT try to download the tutorial data during the course! We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link ([[FsTutorial/Data|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.'''|| ||'''Course Policies''' || ||'''Getting the tutorial data''' || ||Please DO NOT try to download the tutorial data during the course! We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link ([[FsTutorial/Data|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.''' || |
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| [wiki:Self:FsTutorial/Exercises Exercise Overview] | |
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| [wiki:Self:FsTutorial/FileFormats File Formats] | '''Wifi: ''' You may connect to any of the following wifi networks in the classroom area (all networks use the same password): |
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| [wiki:Self:FsTutorial/Tools FreeSurfer Tools] | . '''Name: ''' {{{nmrclass1_wifi_2.4Ghz, nmrclass1_wifi_5Ghz, nmrclass2_wifi_2.4Ghz, nmrclass2_wifi_5Ghz}}} '''Password: ''' {{{brain.map}}} |
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| [wiki:Self:FsTutorial/Glossary Glossary] | === About the Course === 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 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; ## * 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 commands. Only those that appear in a box should be copy-and-pasted into the terminal. They will look like this: {{{ command arg1 arg2 }}} '''''Tip for Mac users''''': The tutorials often refer to keyboard shortcuts (such as Alt+v) which do not work on a Mac. For a list of equivalent keyboard commands on a Mac, please refer to MacCommands. ##||'''Online Question Forum''' ||'''Videos of Lectures''' ||'''Course Evaluation''' || ##||Throughout the course, you may post questions [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|here]] (anonymously or not). || You can find videos of the lectures [[http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA|here]].|| The course evaluation will be posted here on the last day of the course. || ||'''Online Question Forum''' ||'''Videos of Lectures''' || ||Throughout the course, you may post questions [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|here]] (anonymously or not). ||You can find videos of the lectures [[http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA|here]]. || ##Please fill out our course evaluation [[https://docs.google.com/spreadsheet/viewform?formkey=dFJTVm1JOEVXVXZCV25kX0kyMXVkdkE6MA|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. == Course Schedule == ## select one of the course schedules, comment-out the others: ##<<Include(FsTutorial/Jan2009CourseSchedule)>> ##<<Include(FsTutorial/April2009CourseSchedule)>> ##<<Include(FsTutorial/Brazil2009CourseSchedule)>> ##<<Include(FsTutorial/FslCourseSchedule)>> ##<<Include(FsTutorial/MultiModal2009CourseSchedule)>> ##<<Include(FsTutorial/Sept2009CourseSchedule)>> ##<<Include(FsTutorial/Feb2010CourseSchedule)>> ##<<Include(FsTutorial/MultiModal2010CourseSchedule)>> ##<<Include(FsTutorial/StLouis2010CourseSchedule)>> ##<<Include(FsTutorial/Oct2010CourseSchedule)>> ##<<Include(FsTutorial/April2011CourseSchedule)>> ##<<Include(FsTutorial/Brazil2011CourseSchedule)>> ##<<Include(FsTutorial/MultiModal2011CourseSchedule)>> ##<<Include(FsTutorial/June2011FslCourseSchedule)>> ##<<Include(FsTutorial/Dec2011CourseSchedule)>> ##<<Include(FsTutorial/April2012CourseSchedule)>> ##<<Include(FsTutorial/MultiModal2012CourseSchedule)>> ##<<Include(FsTutorial/May2013CourseSchedule)>> ##<<Include(FsTutorial/Nov2013CourseSchedule)>> ##<<Include(FsTutorial/May2014CourseSchedule)>> ##<<Include(FsTutorial/Oct2014CourseSchedule)>> ##<<Include(FsTutorial/BrazilMarch2015CourseSchedule)>> ##<<Include(FsTutorial/MultiModal2015CourseSchedule)>> ##<<Include(FsTutorial/Sept2015CourseSchedule)>> ##<<Include(FsTutorial/April2016CourseSchedule)>> <<Include(FsTutorial/Sept2016CourseSchedule)>> == Additional Useful Information == === During the Course === * [[FsTutorial/Data|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. * Using a Mac & need a text editor? Download gedit, [[http://ftp.gnome.org/pub/GNOME/binaries/mac/gedit/3.2/gedit-3.2.6-3_SnowLeopard_64bit.dmg|here]]. * Some basic information on text editors can be found [[FsTutorial/CreatingTextfiles|here]]. * [[FsTutorial/Scripts|Scripts & aliases]] * [[FsTutorial/Glossary|Glossary]] * '''Taxi''' phone numbers can be found [[http://bpdnews.com/authorized-taxi-companies|here]]. === After the Course === * Home page: http://surfer.nmr.mgh.harvard.edu * A full list of all FreeSurfer [[Tutorials|tutorials]], including ones that may not have been included at this course * [[https://www.zotero.org/freesurfer|Publications]] * Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer * How to cite !FreeSurfer is on the FreeSurferMethodsCitation page. * [[SystemRequirements|System Requirements for Installation]] * [[http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8|iSurf]] - iPhone/iPad app to view !FreeSurfer segmentations ## * [[FsTutorial/SnapShot|PDF and HTML snapshot]] ## * 4pp PDFs: [[attachment:intro4pp.pdf]], [[attachment:recon4pp.pdf]], [[attachment:group4pp.pdf]] [[attachment:feat4pp.pdf]] * [[FsTutorial/Acknowledgements|Acknowledgements]] ## * [[ConferenceRoomA| Conference Room A]] ## * [[FsTutorial/CourseChecklist| Course checklist (internal)]] ## * [[FsTutorial/Exercises|Listing of all exercises]] ## * [[FsTutorial/Tools|FreeSurfer tools]] |
FreeSurfer Tutorial and Workshop
Course Policies |
Getting the tutorial data |
Please DO NOT try to download the tutorial data during the course! 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. |
Wifi: You may connect to any of the following wifi networks in the classroom area (all networks use the same password):
Name: nmrclass1_wifi_2.4Ghz, nmrclass1_wifi_5Ghz, nmrclass2_wifi_2.4Ghz, nmrclass2_wifi_5Ghz Password: brain.map
About the Course
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 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. They will look like this:
command arg1 arg2
Tip for Mac users: The tutorials often refer to keyboard shortcuts (such as Alt+v) which do not work on a Mac. 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. |
Course Schedule
FreeSurfer Course, September 26-29
Copy of all course slides compiled as a book can be found here.
Our awesome FreeSurfer shirts can be purchased here.
8:00 - 9:30am Registration Desk Open
* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream.
** Indicates an optional talk that covers basic/beginner material.
Monday, September 26th - Introduction / Single Subject Analysis / ROI Analysis / MR Acquisition
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
talk/demo |
Zeke Kaufman |
|
9:00 - 9:15 |
talk |
Allison Stevens & Lilla Zöllei |
|
9:15 - 9:30 |
break |
|
|
9:30 - 10:00 |
talk |
Bruce Fischl |
|
10:00 - 11:10 |
talk |
Doug Greve |
|
11:10 - 11:30 |
break |
|
|
11:30 - 11:45 |
Freeview demonstration |
Allison Moreau |
|
11:45 - 12:15 |
tutorial |
||
12:15 - 1:15 |
-- |
-- |
|
1:15 - 1:45 |
tutorial |
||
1:45 - 2:15 |
Surface-based Analysis: Intersubject Registration & Smoothing |
talk |
Lilla Zöllei |
2:15 - 2:35 |
break |
|
|
2:35 - 3:05 |
talk |
Doug Greve |
|
3:05 - 3:55 |
tutorial |
staff |
|
3:55 - 4:25 |
talk |
Dylan Tisdall |
|
4:25 - 4:55 |
talk |
André van der Kouwe |
|
4:55 - 5:15 |
talk |
Dylan Tisdall |
Answers to online questions here
Tuesday, September 27th - Group Analysis / Longitudinal Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
9:00 - 9:50 |
talk |
Emily Lindemer |
|
9:50 - 10:30 |
tutorial |
staff |
|
10:30 - 10:50 |
break |
|
|
10:50 - 11:10 |
talk |
Doug Greve |
|
11:10 - 11:30 |
tutorial |
staff |
|
11:30 - 11:50 |
QDEC demonstration |
demo |
Doug Greve |
11:50 - 12:50 |
Lunch |
-- |
-- |
12:50 - 1:30 |
tutorial |
staff |
|
1:30 - 2:15 |
talk |
Lilla Zöllei |
|
2:15 - 2:55 |
tutorial |
staff |
|
2:55 - 3:25 |
talk |
Bruce Fischl |
|
3:25 - 3:45 |
break |
|
|
3:45 - 4:45 |
tutorial |
staff |
|
4:45 - 5:45 |
Quality Checking a Recon |
demo |
Allison Stevens |
6:30 - ? |
Boston Beer Works |
social activity |
staff |
Answers to online questions here
Boston Beer Works location information here and here.
Meet us in front of Building 149 to catch the 6:30pm shuttle bus (it leaves on time!).
If you miss us, we are taking the MGH/Navy Yard shuttle to North Station. From there, cross the street to get to Canal Street.
Boston Beer Works will be down that street, on your right. (Shuttles depart every 15 minutes up until 7:15pm and every half hour after that).
Wednesday, September 28th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis
Time |
Title |
Type |
Lecturer |
9:00 - 9:30 |
talk |
Lilla Zöllei |
|
9:30 - 10:00 |
tutorial |
staff |
|
10:00 - 10:15 |
talk |
Dylan Tisdall |
|
10:15 - 10:35 |
break |
|
|
10:35 - 11:15 |
talk |
Anastasia Yendiki |
|
11:15 - 12:00 |
tutorial |
staff |
|
12:00 - 1:00 |
Lunch |
-- |
-- |
1:00 - 2:00 |
talk |
Anastasia Yendiki |
|
2:00 - 3:00 |
tutorial |
staff |
|
3:00 - 3:10 |
talk |
Anastasia Yendiki |
|
3:10 - 3:30 |
break |
|
|
3:30 - 4:30 |
talk |
Jon Polimeni |
|
4:30 - 5:10 |
talk |
Doug Greve |
Answers to online questions here
Thursday, September 29th - fMRI Analysis / Multimodal Analysis / Future Directions
Time |
Title |
Type |
Lecturer |
9:00 - 9:40 |
talk |
Doug Greve |
|
9:40 - 10:40 |
tutorial |
staff |
|
10:40 - 11:00 |
break & Evaluation |
|
|
11:00 - 11:30 |
talk |
Doug Greve |
|
11:30 - 12:00 |
Multi-Modal Integration Tutorial: fMRI Integration & Surface-based Group fMRI Analysis |
tutorial |
staff |
12:00 - 1:00 |
Lunch |
-- |
-- |
1:00 - 1:40 |
talk |
Lilla Zöllei |
|
1:40 - 2:25 |
Future Directions |
talk |
Bruce Fischl |
2:25 - 2:45 |
Question & Answer Session |
-- |
staff |
Answers to online questions here
* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream.
** Indicates an optional talk covering basic/beginner material.
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.
Using a Mac & need a text editor? Download gedit, here.
Some basic information on text editors can be found here.
Taxi phone numbers can be found here.
After the Course
Home page: http://surfer.nmr.mgh.harvard.edu
A full list of all FreeSurfer tutorials, including ones that may not have been included at this course
Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
iSurf - iPhone/iPad app to view FreeSurfer segmentations