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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, lcn_guest2, lcn_guest5
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

Spring 2020 FreeSurfer Course: March 30th - April 2nd

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.
*** Indicates optional extra time to work on tutorials and/or ask questions about your own data.

Research backgrounds of past and present staff members can be found on the LCN website.

Monday, March 30th - Introduction / Single Subject Analysis / ROI Analysis

Time	Title	Type	Lecturer
8:30 - 8:40	** Intro to Linux for FreeSurfer Users	talk/demo	Matthew Larrabee
8:40 - 9:00	** Unix for FreeSurfer Users	tutorial
9:00 - 9:15	** Intro to FreeSurfer Jargon	talk	Caroline Magnain
9:15 - 9:25	break
9:25 - 10:10	Introduction to Freesurfer	talk	Bruce Fischl
10:10 - 11:20	Analyzing the Individual Subject	talk	Doug Greve
11:20 - 11:40	break
11:40 - 12:00	Freeview demonstration	demo	Bram Diamond
12:00 - 12:30	Introduction to FreeSurfer Output	tutorial	staff
12:30 - 1:30	Lunch (Suggestions for where to eat)
1:30 - 1:45	Introduction to FreeSurfer Output	tutorial	staff
1:45 - 2:15	Surface-based Analysis: Intersubject Registration & Smoothing	talk	Diyva Varadarajan
2:15 - 2:35	break
2:35 - 3:05	ROI Analysis	talk	Doug Greve
3:05 - 3:50	ROI Analysis Tutorial	tutorial	staff
3:50 - 4:20	Structural & Functional Data Integration	talk	David Salat
4:20 - 4:50	Practice Working with Data	tutorial	staff

Answers to online questions here

Tuesday, March 31st - Group Analysis / Longitudinal Analysis / Troubleshooting

Time	Title	Type	Lecturer
8:00 - 9:00	*** Morning Help Session		research technicians
9:00 - 9:45	Group Analysis	talk	Viviana Siless
9:45 - 10:25	Group Analysis Tutorial (FSGD Examples)	tutorial	staff
10:25 - 10:45	break
10:45 - 11:30	FreeSurfer Troubleshooting	talk	Bruce Fischl
11:30 - 12:30	Troubleshooting Tutorial	tutorial	staff
12:30 - 1:30	Lunch
1:30 - 2:15	Quality Checking a Recon	talk	Leah Morgan
2:15 - 2:55	Multiple Comparisons	talk	Doug Greve
2:55 - 3:25	Multiple Comparisons Tutorial	tutorial	staff
3:25 - 4:05	break
4:05 - 4:50	Longitudinal FreeSurfer	talk	Malte Hoffmann
4:50 - 5:30	LongitudinalTutorial	tutorial	staff
5:30 - 7:30	Social Night in the atrium of Bldg. 149	Snacks and Beverages Served

Answers to online questions here

Wednesday, April 1st - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Time	Title	Type	Lecturer
8:00 - 9:00	*** Morning Help Session		research technicians
9:00 - 9:30	* Intro to MR (SpinBench)	talk	Robert Frost
9:30 - 10:00	Multi-Modal Integration, Part 1: Registration	talk	Aina Frau-Pascual
10:00 - 10:30	Multi-Modal Integration Tutorial, Part 1	tutorial	staff
10:30 - 10:50	break
10:50 - 11:05	* Intro to Diffusion MRI Physics	talk	Robert Frost
11:05 - 11:45	Introduction to Diffusion MRI	talk	Anastasia Yendiki
11:45 - 12:30	Diffusion Processing Tutorial	tutorial	staff
12:30 - 1:30	Lunch	--	--
1:30 - 2:20	Tracts Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
2:20 - 3:20	TRACULA Tutorial	tutorial	staff
3:20 - 3:40	break
3:40 - 3:50	Longitudinal TRACULA	talk	Anastasia Yendiki
3:50 - 4:50	Basics of fMRI Analysis	talk	Jingyuan Chen
4:50 - 5:30	* MRI Acquisition Methods	talk	Andre van der Kouwe

Answers to online questions here The FreeSurfer Evaluation is here!

Thursday, April 2nd - fMRI Analysis / Multimodal Analysis / Future Directions

Time	Title	Type	Lecturer
8:00 - 9:00	*** Morning Help Session		research technicians
9:00 - 9:30	FSFAST, Part 1: Preprocessing	talk	Doug Greve
9:30 - 10:00	FSFAST Tutorial, Part 1	tutorial	staff
10:00 - 10:20	break & Evaluation
10:20 - 11:20	FSFAST, Part 2: GLM Analysis	talk	Doug Greve
11:20 - 12:00	FSFAST Tutorial, Part 2	tutorial	staff
12:00 - 1:00	Lunch
1:00 - 1:30	* An Overview of Registration Methods	talk	Lilla Zöllei
1:30 - 1:45	Resting State fMRI	talk	Doug Greve
1:45 - 2:15	Multi-Modal Integration, Part 2: Group Analysis	talk	Doug Greve
2:15 - 3:00	Multi-Modal Integration Tutorial, Part 2	tutorial	staff
3:00 - 3:15	break
3:15 - 3:30	* FreeSurfer vs. VBM	talk	Doug Greve
3:30 - 4:30	* Future Directions	talk	FS Development Team
4:30 - 5:00	Question & Answer Session		staff

Answers to online questions here
FreeSurfer Merchandise Enjoyed our course? 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.
Using a Mac & need a text editor? Download gedit, here.
Some basic information on text editors can be found here.
Scripts & aliases
Glossary
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
Publications
How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
System Requirements for Installation
iSurf - iPhone/iPad app to view FreeSurfer segmentations

Acknowledgements

-  ⇤ ← Revision 134 as of 2013-05-10 11:52:57 → 
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-Deletions are marked like this.
+Additions are marked like this.
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-<<TableOfContents>>
+== WARNING: The hyperlinks in the tables below used to download slides will NOT WORK in Google Chrome. Please use a different browser to access these slides. ==
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-== 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 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:
+##||||'''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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+Line 13:
- * 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.
-Line 15:
+Line 14:
-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:
+=== Wifi ===
You may connect to any of the following wifi networks in the classroom area (all networks use the same password):
 Line 17:
-----
+ '''Name: ''' {{{nmrclass1_wifi_2.4Ghz,  nmrclass1_wifi_5Ghz,  lcn_guest2,  lcn_guest5}}}

 '''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).

##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:
-Line 21:
+Line 34:
-----
'''Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!'''
+'''''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.
-Line 24:
+Line 36:
-== 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.'''
+##||'''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]]. ||
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-== 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.
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+Line 42:
-== Course Evaluation ==
Please fill out our course evaluation [[ https://docs.google.com/spreadsheet/viewform?formkey=dF9vNnlCUHVuQ1BsUmREdDRwVnBHS0E6MA|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.
+##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.
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-<<Include(FsTutorial/May2013CourseSchedule)>>
+##<<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)>>
##<<Include(FsTutorial/April2017CourseSchedule)>>
##<<Include(FsTutorial/Sept2017CourseSchedule)>>
##<<Include(FsTutorial/April2018CourseSchedule)>>
##<<Include(FsTutorial/Spring2019CourseSchedule)>>
##<<Include(FsTutorial/Fall2019CourseSchedule)>>
<<Include(Spring2020CourseSchedule)>>
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+=== 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 ===
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- * Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
 * [[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.
 * [[FsTutorial/Scripts|Scripts & aliases mentioned during Unix talk]]
 * [[FsTutorial/Glossary|Glossary]]
 * [[Publications]]
+ * A full list of all [[Tutorials|FreeSurfer tutorials]], including ones that may not have been included at this course
 * [[https://www.zotero.org/freesurfer|Publications]]
 * How to cite !FreeSurfer is on the FreeSurferMethodsCitation page.
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+Line 94:
- * '''Taxi''' Phone numbers can be found [[http://www.cityofboston.gov/police/hackney/companies.asp|here]].
 * How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
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- * if you are using your own mac it might be helpful to download gedit.  Gedit can be downloaded here: http://ftp.gnome.org/pub/GNOME/binaries/mac/gedit/3.2/gedit-3.2.6-3_SnowLeopard_64bit.dmg
+## === Temporary Instructions (Ignore) ===
## {{{
## rsync -tv rsync://surfer.nmr.mgh.harvard.edu/pub/data/course_data/fs_update $FREESURFER_HOME/bin/ && rm -rf ~/tutorial_data && fs_update &&  fs_tutorial_data --delete
## }}}