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| '''Laptop damage policy: 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.''' == 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://docs.google.com/spreadsheet/viewform?formkey=dDNaOUNxUF90NDJJOWdLNUx3Z2RiMHc6MA|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 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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| == Videos of Lectures == You can find videos of the lectures [[http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA|here]]. |
=== 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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| == 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: |
'''Name: ''' {{{nmrclass1_wifi_2.4Ghz, nmrclass1_wifi_5Ghz, lcn_guest2, lcn_guest5}}} |
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| * 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. |
'''Password: ''' {{{brain.map}}} |
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| 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: | === 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). |
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| ---- | ##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: |
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| ---- | '''''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. |
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| == Commands on a Mac == 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]]. || |
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| ##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/Nov2013CourseSchedule)>> | ##<<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(FsTutorial/Spring2020CourseSchedule)>> |
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| * [[FsTutorial/Scripts|Scripts & aliases mentioned during Unix talk]] | * Some basic information on text editors can be found [[FsTutorial/CreatingTextfiles|here]]. * [[FsTutorial/Scripts|Scripts & aliases]] |
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| * '''Taxi''' Phone numbers can be found [[http://www.cityofboston.gov/police/hackney/companies.asp|here]]. |
* '''Taxi''' phone numbers can be found [[http://bpdnews.com/authorized-taxi-companies|here]]. |
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| * [[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 |
* 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]] |
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## === 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 ## }}} |
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
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
How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
iSurf - iPhone/iPad app to view FreeSurfer segmentations