|
Size: 13201
Comment:
|
Size: 12989
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| The virtual !FreeSurfer course is scheduled for '''September 14-15th, 2022'''. This is a two day course that offers a basic introduction to !FreeSurfer. A !FreeSurfer Virtual Machine (VM) will be provided to course participants so that they can easily work with !FreeSurfer and practice data during the course. Before registering, review the tentative [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|schedule]] to make sure it will work for you and review the [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|technical requirements]] to be sure your computer can run the course software. You will be required to verify your computer can properly host the course software by Sept 7th in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you. | The virtual !FreeSurfer course is scheduled for '''September 14-15th, 2022'''. This is a two day course that offers a basic introduction to !FreeSurfer. A !FreeSurfer Virtual Machine (VM) will be provided to course participants so that they can easily work with !FreeSurfer and practice data during the course. Before registering, review the tentative [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|schedule]] to make sure it will work for you and review the [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|technical requirements]] to be sure your computer can run the course software. You will be required to verify your computer can properly host the course software by '''Sept 7th''' in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you. |
| Line 8: | Line 8: |
| '''Registration is now open for the Fall 2022 Virtual FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>> | '''Registration is now open for the Fall 2022 Virtual !FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>> |
| Line 11: | Line 11: |
| Cancellation deadline: '''August 31st, 2022''' <<BR>> Computer verification deadline: '''September 7th, 2022''' |
|
| Line 12: | Line 14: |
| If you have a specific question about the !FreeSurfer courses that was not answered by this website and our [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] or would like to host a course in your area, you can email one of the course organizers, Allison Stevens or Liam Sennott (freesurferlab@gmail.com). | If you have a specific question about the !FreeSurfer courses that was not answered by this website and our [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] or would like to host a course in your area, you can email one of the course organizers (fscourse AT nmr.mgh.harvard.edu). |
| Line 18: | Line 21: |
| '''Click on any of the topics below for more information: <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Overview|Overview]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|Schedule]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Payment|Payment]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseTopics|Topics Covered During the Course]] <<BR>> ''' |
'''Click on any of the topics below for more information: <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Overview|Overview]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Schedule|Schedule]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Payment|Payment]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#FAQ|FAQ]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#CourseTopics|Topics Covered During the Course]] <<BR>> ''' |
| Line 28: | Line 34: |
| ||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Allison, and Lillia or Caroline if they want? || ||9:15 - 10:00 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Doug or Bruce Fischl || |
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Allison || ||9:15 - 10:00 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl || |
| Line 34: | Line 40: |
| ||12:00 - 12:45 ||[[FsTutorial/OutputData_freeview|Individual Subject Output]] ||tutorial || Allison, RA#2 RA#3 || | ||12:00 - 12:45 ||[[FsTutorial/OutputData_freeview|Individual Subject Output]] ||tutorial || staff || |
| Line 37: | Line 43: |
| ||2:15 - 3:00 ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||RA#1 RA#2 RA#3 || | ||2:15 - 3:00 ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||staff || |
| Line 39: | Line 45: |
| ||3:15 - 4:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk || Allison? Bruce?|| ||4:00 - 5:00 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Freesurfer]] ||tutorial ||Dev, Allison, RA#3|| ||5:00 - 5:45 || QA Demo ||talk || Allison? Leah? || |
||3:15 - 4:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk || Doug Greve || ||4:00 - 5:00 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Freesurfer]] ||tutorial ||staff|| ||5:00 - 5:45 || Quality Checking a Recon ||talk || tbd || |
| Line 43: | Line 49: |
| ** optional talks | |
| Line 46: | Line 53: |
| ||10:00 - 10:30 || Surface Based Analysis ||talk || Divya / Doug || | ||10:00 - 10:30 || Surface Based Analysis ||talk || tbd || |
| Line 49: | Line 56: |
| ||11:30 - 12:10 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial || RA#1 RA#2 RA#3 || | ||11:30 - 12:10 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial || staff || |
| Line 51: | Line 58: |
| ||1:10 - 1:55 || Corrections for MC ||talk || Doug || ||1:55 - 2:25 || Tutorial: Corrections ||tutorial ||RA#1 RA#2 RA#3 || |
||1:10 - 1:55 || Corrections for Multiple Comparisons ||talk || Doug || ||1:55 - 2:25 || Tutorial: Corrections ||tutorial ||staff || |
| Line 54: | Line 61: |
| ||3:40 - 4:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte? Doug?|| ||4:15 - 4:55 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||Dev, RA#2 RA#3 || ||4:55 - 5:15 || Q&A with FreeSurfer Team||talk || Doug? Bruce?|| |
||3:40 - 4:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||tbd|| ||4:15 - 4:55 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff || ||4:55 - 5:15 || Q&A with FreeSurfer Team||talk || staff|| |
| Line 66: | Line 73: |
| Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash)<<BR>> As long as there are empty spots in the course, we will accept late registrations (regardless of the cancellation deadline). <<BR>> Payment and all questions about payment should be sent to Stacey. |
|
| Line 68: | Line 79: |
| Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash) As long as there are empty spots in the course, we will accept late registrations (regardless of the cancellation deadline). Payment and all questions about payment should be sent to Stacey. |
|
| Line 73: | Line 81: |
| Cancellation deadline: '''August 31st, 2022''' <br> | Course fees are refundable, minus a $100 fee, up to 2 weeks prior to the program. If you verify your computer is ''unable'' to host the course software & data by September 7th, you will be issued a full refund. If you do not cancel your registration by August 31st or do not show your computer is unable to run the software by September 7th, you will not be issued a refund. Cancellation deadline: '''August 31st, 2022''' <<BR>> |
| Line 76: | Line 86: |
| Course fees are refundable, minus a $100 fee, up to 2 weeks prior to the program. If you verify your computer is ''unable'' to host the course software & data by September 7th, you will be issued a full refund. If you do not cancel your registration by August 31st or do not show your computer is unable to run the software by September 7th, you will not be issued a refund. | |
| Line 78: | Line 87: |
==== Cancellations ==== Course fees are refundable up to the cancellation deadline. A $100 fee will be deducted, should you request a refund up to 2 weeks prior to the program. Course fees are refundable minus a $100 fee up to 2 weeks prior to the program. If you verify your computer is unable to host the course software & data by September 7th, you will be issued a full refund. ##After that, the tuition can be applied to a future program within one year of the course for which you registered and paid for, or you can send someone in your place. ==== FAQ's ==== |
=== FAQ === |
| Line 91: | Line 94: |
| 1. '''I cannot pay by check or credit card. Do I have any other options?''' * If you are local, you may bring a cash payment to Allison Stevens (astevens at nmr dot mgh dot harvard dot edu) before the deadline. If you are not local, you can pay via Western Union and Moneygram if it is addressed to Stacey Ladieu. Please contact Stacey (sladieu at nmr dot mgh dot harvard dot edu) first for details. 1. '''Payment is required with registration but my institution will take several weeks to cut a check. Does this mean I cannot attend?''' * You may still attend the course. Have the person at your institution that is responsible for arranging your payment contact Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu) to verify that a request for payment has been submitted and is being processed. |
1. '''I cannot pay by internal fund or credit card. Do I have any other options?''' * If you are local, you may bring a cash payment to Allison Stevens (astevens at nmr dot mgh dot harvard dot edu) before the deadline. If you are not local, you may be able to pay via Western Union and Moneygram if it is addressed to Stacey Ladieu. Please contact Stacey (sladieu at nmr dot mgh dot harvard dot edu) first for details. ## 1. '''Payment is required with registration but my institution will take several weeks to cut a check. Does this mean I cannot attend?''' ## * You may still attend the course. Have the person at your institution that is responsible for arranging your payment contact Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu) to verify that a request for payment has been submitted and is being processed. |
| Line 102: | Line 105: |
| * Sure! But please know that if you show us during a tutorial, questions from students about that tutorial will have to take priority over personal data questions. If you email Allison or Emma prior to the course, they can try to arrange some help. | * Sure! But please know that if you show us during a tutorial, questions from students about that tutorial will have to take priority over personal data questions. If you email the course organizers (fscourse AT nmr.mgh.harvard.edu) prior to the course, they can try to arrange a time to discuss your data. |
| Line 104: | Line 107: |
| * Sure! Please see the response to the question above. | * Sure! Please email the course organizers (fscourse AT nmr.mgh.harvard.edu) for assistance. |
| Line 107: | Line 110: |
| ==== Course Topics ==== | === Course Topics === |
| Line 118: | Line 121: |
| * '''Interaction with Individual Subject Data - Tutorial''' | * '''Freeview demonstration''' * A live walk-through for how to use the Freeview GUI. * '''Interaction with Individual Subject Output - Tutorial''' |
| Line 120: | Line 125: |
| * '''A Non-physicist's Intro to MR (optional)''' * A short introduction to the basic processes underlying MR imaging, with an emphasis on intuitive explanations for non-physicist MR users. |
## * '''A Non-physicist's Intro to MR (optional)''' ## * A short introduction to the basic processes underlying MR imaging, with an emphasis on intuitive explanations for non-physicist MR users. |
| Line 124: | Line 129: |
| * '''Structural and Functional Integration''' * An explanation of why structural information is critical for functional imaging research. * '''Failure Modes and Troubleshooting with !FreeSurfer - Talk and Tutorial''' |
## * '''Structural and Functional Integration''' ## * An explanation of why structural information is critical for functional imaging research. * '''Region of Interest (ROI) Analysis - Talk and Tutorial ''' * A description of the !FreeSurfer atlases used in subcortical segmentation and cortical parcellation as well as the measures !FreeSurfer provides. Information on creating and analyzing ROIs (volume vs. intensity studies). * '''!FreeSurfer Troubleshooting - Talk and Tutorial''' |
| Line 132: | Line 139: |
| * '''Region of Interest (ROI) Analysis - Talk and Tutorial ''' * A description of the !FreeSurfer atlases used in subcortical segmentation and cortical parcellation as well as the measures !FreeSurfer provides. Information on creating and analyzing ROIs (volume vs. intensity studies). |
|
| Line 136: | Line 141: |
| * '''QDEC (group analysis software) - Talk and Tutorial''' * Introduction to a user-friendly tool for conducting group analyses. * '''Multi-Modal Integration - Talk and Tutorial''' * Introduction on how !FreeSurfer output can be used with other modalities (i.e. fMRI data, diffusion data) |
## * '''QDEC (group analysis software) - Talk and Tutorial''' ## * Introduction to a user-friendly tool for conducting group analyses. ## * '''Multi-Modal Integration - Talk and Tutorial''' ## * Introduction on how !FreeSurfer output can be used with other modalities (i.e. fMRI data, diffusion data) * '''Longitudinal Analysis in !FreeSurfer''' * How to process longitudinal data with !FreeSurfer and what's going on behind the scenes. |
Virtual FreeSurfer Course
The virtual FreeSurfer course is scheduled for September 14-15th, 2022. This is a two day course that offers a basic introduction to FreeSurfer. A FreeSurfer Virtual Machine (VM) will be provided to course participants so that they can easily work with FreeSurfer and practice data during the course. Before registering, review the tentative schedule to make sure it will work for you and review the technical requirements to be sure your computer can run the course software. You will be required to verify your computer can properly host the course software by Sept 7th in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you.
Registration is now open for the Fall 2022 Virtual FreeSurfer Course! Click here to register!
Cancellation deadline: August 31st, 2022
Computer verification deadline: September 7th, 2022
If you have a specific question about the FreeSurfer courses that was not answered by this website and our FAQ or would like to host a course in your area, you can email one of the course organizers (fscourse AT nmr.mgh.harvard.edu).
Course Details
Click on any of the topics below for more information:
Overview
Schedule
Payment
FAQ
Topics Covered During the Course
Overview
The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials.
Schedule
Wednesday, September 14th - Introduction / Single Subject Analysis / ROI Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
** Intro to Linux for FreeSurfer Users |
talk/demo |
Dev |
9:00 - 9:15 |
talk |
Allison |
|
9:15 - 10:00 |
talk |
Bruce Fischl |
|
10:00 - 10:15 |
break |
|
|
10:15 - 11:25 |
talk |
Doug Greve |
|
11:25 - 11:45 |
Jackson |
||
11:45 - 12:00 |
break |
|
|
12:00 - 12:45 |
tutorial |
staff |
|
12:45 - 1:45 |
Lunch |
||
1:45 - 2:15 |
talk |
Doug Greve |
|
2:15 - 3:00 |
tutorial |
staff |
|
3:00 - 3:15 |
break |
|
|
3:15 - 4:00 |
talk |
Doug Greve |
|
4:00 - 5:00 |
tutorial |
staff |
|
5:00 - 5:45 |
Quality Checking a Recon |
talk |
tbd |
** optional talks
Thursday, September 15th - Group Analysis / Longitudinal Analysis
Time |
Title |
Type |
Lecturer |
10:00 - 10:30 |
Surface Based Analysis |
talk |
tbd |
10:30 - 11:15 |
talk |
Doug |
|
11:15 - 11:30 |
break |
|
|
11:30 - 12:10 |
tutorial |
staff |
|
12:10 - 1:10 |
Lunch |
||
1:10 - 1:55 |
Corrections for Multiple Comparisons |
talk |
Doug |
1:55 - 2:25 |
Tutorial: Corrections |
tutorial |
staff |
2:25 - 3:40 |
break |
|
|
3:40 - 4:15 |
talk |
tbd |
|
4:15 - 4:55 |
tutorial |
staff |
|
4:55 - 5:15 |
Q&A with FreeSurfer Team |
talk |
staff |
Payment
Cost
The fee for the course is $400. A reduced rate of $275 is available to undergraduate and graduate students. MDs, PhDs, RAs and Post-docs do not qualify for the student rate!
Accepted Payment Types
Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash)
As long as there are empty spots in the course, we will accept late registrations (regardless of the cancellation deadline).
Payment and all questions about payment should be sent to Stacey.
Payment Coordinator/Contact: Stacey Ladieu (sladieu at martinos dot org)
Cancellations, Refunds, and Deadlines
Course fees are refundable, minus a $100 fee, up to 2 weeks prior to the program. If you verify your computer is unable to host the course software & data by September 7th, you will be issued a full refund. If you do not cancel your registration by August 31st or do not show your computer is unable to run the software by September 7th, you will not be issued a refund.
Cancellation deadline: August 31st, 2022
Computer verification deadline: September 7th, 2022
FAQ
How many individuals are accepted into the Virtual course?
- 20 people
Do postdocs qualify for the student rate?
- No, sorry.
Is there a discount for MGH or Martinos Center employees?
- Sorry, no.
I cannot pay by internal fund or credit card. Do I have any other options?
- If you are local, you may bring a cash payment to Allison Stevens (astevens at nmr dot mgh dot harvard dot edu) before the deadline. If you are not local, you may be able to pay via Western Union and Moneygram if it is addressed to Stacey Ladieu. Please contact Stacey (sladieu at nmr dot mgh dot harvard dot edu) first for details.
The course is full. Can you register me for the next one?
You can sign up for our course mailing list and you will be notified when registration for the next course opens (that list is here). You can also register for the currently full course to be put on the waiting list for it. This does not however automatically get you a spot in the next course.
Can I get a receipt for the course?
- Contact the payment coordinator, Stacey (sladieu at nmr dot mgh dot harvard dot edu) to arrange getting a receipt.
How do I know if my payment went through?
- If it hasn't we will contact you.
I have some data I would like to get your opinion on. Can I show it to you?
- Sure! But please know that if you show us during a tutorial, questions from students about that tutorial will have to take priority over personal data questions. If you email the course organizers (fscourse AT nmr.mgh.harvard.edu) prior to the course, they can try to arrange a time to discuss your data.
I need some help installing FreeSurfer on my laptop - I can't seem to get it to work. Can you help with that?
- Sure! Please email the course organizers (fscourse AT nmr.mgh.harvard.edu) for assistance.
Course Topics
Below is the list of topics. The course format is composed of lectures followed by hands-on tutorials so that you can gain experience interacting with data processed by FreeSurfer. A basic understanding of Linux is necessary to run and work with FreeSurfer.
Linux Demo/Tutorial (optional)
This Linux tutorial is very basic. Scripting will not be covered. This tutorial will cover how to to navigate (cd) through directories, how to copy files, how to make directories, how to use emacs, and how to set variables. For those who are not familiar with Linux, this tutorial is meant to get you comfortable enough to at least get through the FreeSurfer tutorials that are part of the course. If you have never used Linux before, this session is highly recommended.
Introduction to FreeSurfer Jargon (optional)
- Intended for those new to imaging software. Explains basic vocabulary such as voxel, surface, vertex, volume, segmentation, parcellation, registration, and recon.
Introduction to FreeSurfer
Overview of FreeSurfer's abilities.
Analyzing the Individual Subject in FreeSurfer
Description of each step of the FreeSurfer processing stream.
Freeview demonstration
- A live walk-through for how to use the Freeview GUI.
Interaction with Individual Subject Output - Tutorial
Using FreeSurfer's visualization tools to look at FreeSurfer output.
Region of Interest (ROI) Analysis - Talk and Tutorial
A description of the FreeSurfer atlases used in subcortical segmentation and cortical parcellation as well as the measures FreeSurfer provides. Information on creating and analyzing ROIs (volume vs. intensity studies).
FreeSurfer Troubleshooting - Talk and Tutorial
Discussion of the possible errors one may find in their FreeSurfer output and how to fix them.
Quality Checking a Recon
Live demo of how to scroll through FreeSurfer output and look for errors.
Surface-based Analysis: Intersubject Registration & Smoothing
- Volume vs. Surface-based analysis
Group Analysis/GLM/Multiple Comparisons (mri_glmfit)- Talk and Tutorial
- Covers the basics of group analysis in the context of imaging data.
Longitudinal Analysis in FreeSurfer
How to process longitudinal data with FreeSurfer and what's going on behind the scenes.
Question and Answer Session
- Open forum to resolve any unanswered questions
Course Mailing List
SUBSCRIBE:
If you are interested in being notified about future course offerings, sign up for our mailing list (here).
UNSUBSCRIBE:
To unsubscribe from the course mailing list please click here.