1. Course Checklist

See also: OrganizingFSCourse

Before announcing course (2.5 months before course):

Class set up for Environmental Services -
Room set up as follows:
4 rows of 3 tables and 1 row of 2 tables where the pole is located. (total of 28 seats at the tables)
1 row of 8 chairs along the right side of the room and 1 row of 8 chairs in the back of the room.
3 tables out the room with 2 chairs.
One easel at the front of the room.
2 chairs at the front of the room.

After sending out course announcement:

5 weeks before the course:

4 weeks before course:

3 weeks before course:

2 weeks before the course: *check on payment status for those bumped up from the waiting list

1 week before the course:

A few days before the course:

Course set up:

Computers:

Day of course:

After:

2. E-mails

Giving Course Mailing List Advanced Notice

Subject: FreeSurfer Course Registration Opening soon!!

Just wanted to give you all the heads up that we will be opening registration for the April FreeSurfer course either tonight or tomorrow.

This list will get a chance to sign up for course two days before registration is opened up to the rest of the world so keep your eye on your email!

Allison

If you no longer wish to receive these emails, please reply to this message with UNSUBSCRIBE in the body of the email.


Announcing course:

Subject: Registration for Upcoming Freesurfer Course, Sept. 17 & 18

The Freesurfer group will be offering a three-day Freesurfer Tutorial and Workshop April 4-6 at the Martinos Center in Charlestown, MA. A description of the course and a list of the topics covered can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

**Please note the expansion of the course and the new registration fee.**

If after reading the details on the website above, you decide to take the April course, please fill out the registration form here: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.april11.cgi

There is room for only 34 participants and registration is on a first-come, first-serve basis. If you are not one of the first 34, you will be put on a waiting list and will be notified if a spot becomes available.

The link above also has information about arranging payment for the course, accommodations, course location, as well as a tentative schedule. If you do not arrange payment of the course fee by the deadline, your spot will be released. Please refrain from registering for the course before you have verified that you or your institution can meet the payment requirements.

Regards,
The FreeSurfer Team


To those who registered:

Subject: Thank you for registering for the FS course!

Please refer to the website below to arrange payment of your registration fee (Note: Check is the *only* method of payment we can receive). Payment must be received by *September 13th*. All questions about payment should go to Stacey Ladieu, sladieu@nmr.mgh.harvard.edu. Please feel free to CC me so I know to check you off as starting the payment process.

Information about a nearby hotel with a special rate is also listed on the page below:

http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Accommodations

If for any reason, you cannot attend the course please let me know as soon as possible. Thanks again and you will hear from me again in a few weeks about preparation for the course.
Allison


To those on the waiting list:

Subject: FreeSurfer Course waiting list

Hi, You have been placed on the waiting list for the April FreeSurfer course. As soon as a spot becomes available, I will email the first person on the waiting list and give that person a day to respond about whether s/he would like the spot. If I don't hear back, I move on to the next person on the list. I apologize that I do not give more time for a response but usually the spots open up a week or two before the course.

Every FreeSurfer course we have had so far has had *at least* one spot open up and usually more so I think it is safe to be fairly optimistic about the possibility of getting into this course.

Please also be aware that check is the only form of payment we can accept for the registration fee.
Allison


If have not sent payment yet:

Subject: FreeSurfer Course Payment

Hello everyone,
We have not yet received your payment for the October FreeSurfer course. The deadline for arranging payment is this Monday, September 13th. If we do not receive your payment, your spot will be given to someone on the waiting list.

If you have sent in your payment already or have made arrangements with Stacey, please let me know as you may have been placed on this list accidentally. If I do not hear from you by the end of Monday, then I will have to give away your spot.

Thanks,
Allison


To those who have not paid on payment deadline:

Subject: FreeSurfer Course Payment not received

Hello, Today is the payment deadline for the FreeSurfer course registration fee. We have not heard from you about arranging payment for the course. If I do not hear from you by the end of today, I will have to give your spot up to the next person on the waiting list. Allison


To person on waiting list being offered spot:

Subject: Open Spot in FreeSurfer Course

A spot has opened up for the April FreeSurfer course. Please let me know by the end of the day whether you would like this spot. If I do not hear from you, I will offer the spot to the next person on the waiting list tomorrow morning.

Information about the course can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

Please be sure that you will be able to arrange payment for the course by check before you accept the spot. Allison


To those on waiting list offered a spot who respond (they have until the end of the day to respond):

Please refer to the website below to arrange payment of your registration fee (Note: credit cards are not accepted). All questions about payment should go to Stacey Ladieu, sladieu@nmr.mgh.harvard.edu. Please let me know when you have mailed the check so I know to keep your spot.

Information about a nearby hotel with a special rate is also listed on the page below:

http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Accommodations

I will send out more information about the course in the coming weeks.
Allison


To auditors: (**change link to schedule**)

Subject: FreeSurfer Course auditors

Hello all,
You signed up to audit the FreeSurfer Course on October 4th & 5th. The course is held in Conference room A of Building 149.

Directions to this location are here:
http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Directions

If you are driving to the Center and would like to purchase parking stickers ($5 for each 24 hour sticker), please read the Parking section of the website above and let me know how many stickers you need.

The course schedule can be found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Feb2010CourseSchedule

Unfortunately, as an auditor, you cannot participate in any of the tutorials or one-on-one sessions. If you have questions about installing FreeSurfer or processing data, please send those to the FreeSurfer mailing list. One exception is that the UNIX talk/tutorial can be attended by auditors. It is a very basic tutorial for individuals who have never used FreeSurfer or Unix before. Scripting is not covered during this talk. Auditors with no UNIX experience may find this helpful. It starts at 8am *sharp*.

On the days of the course, you will find a row of chairs in the back of the room where you can sit. If I haven't met you, please introduce yourself to me at some point during the course so I know you came. No one ever remembers to do this - but please do, otherwise I may give your spot away to someone else if I think you didn't show.

If for any reason you do not plan to attend the course or plan to attend only a few lectures, let me know so I'm aware of how much room there is for others.

If you have any questions, please let me know.
Allison


To auditors and registrants:

Subject: FreeSurfer Course Announcement - Course Prep

Hi everyone,
We often get questions on how to prepare for the course, especially if you are new to FreeSufer. Below are some suggestions:

COURSE MATERIALS
In general, feel free to go through any of the slides and tutorials that we'll be covering during the course. They can be found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/April2011CourseSchedule

Not all of the slides are up or updated yet, but feel free to look at what is there (what was presented during the last course).

UNIX
If you are unfamiliar with UNIX, it may help to do this online tutorial:
http://www.ee.surrey.ac.uk/Teaching/Unix/
Other good UNIX references are:
http://www.fmrib.ox.ac.uk/fslcourse/unix_intro/
http://docstore.mik.ua/orelly/linux/lnut/index.htm

SCRIPTING
Scripting will not be covered during the course, but following are some good references:
http://www.linuxjournal.com/article/1299
https://supportweb.cs.bham.ac.uk/documentation/tutorials/docsystem/build/tutorials/unixscripting/unixscripting.html

MR
If you are unfamiliar with MR physics, you can read up on it here:
http://www.cis.rit.edu/htbooks/mri/

FREESURFER
You can read up on the techniques and applications of FreeSurfer here (found under the References section):
https://surfer.nmr.mgh.harvard.edu/fswiki/

You can download FreeSurfer and process your own data. Instructions on installation are here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

Instructions for processing your data are at the bottom of this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer

*Note* - there is an optional session on the first day of the course to get help with installation and/or processing. We suggest trying it on your own first so we can be prepared for any obstacles you may encounter.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

We'll go over these topics at the course, but it might help to get an introduction to them beforehand. Let me know if there is anything else you think would be helpful to know before the course.

Finally, please note the deadline has passed to get a refund for cancelling your registration. If you cannot make it to the course, please let me know as soon as possible so we can give your spot to someone on the waiting list. Allison


To lab: Hi everyone, Just wanted to give you the heads up that we'll be holding another FreeSurfer course on April 4th through 6th. This one will cover more topics than our previous courses so even if you've attended them before, there may be some new material on the schedule that you are interested in. You can find that here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/April2011CourseSchedule

The times might still shift around a bit so be sure to check them again the day before.

If you're interested in attending some of the lectures, let me know just so I have an idea of how many chairs I should have out. The chairs in the back are for the auditors but I'll have chairs along the side of the room for staff.

Allison p.s. Savoy's fMRI course is going on now and his Multimodal course is happening in May. He allows some auditors if anyone is interested: http://www.nmr.mgh.harvard.edu/martinos/training/fMRIVisitFellowProg.php http://www.nmr.mgh.harvard.edu/martinos/training/multimodalImaging.php


To registrants: (**maybe not send any more since we just get a book?**)

Subject: FreeSurfer Course Announcement - Parking

Parking near the Center is difficult to get and is either metered (with a 2 hour limit) or expensive ($20+/day for a garage). We can get discounted parking for a group at $5/day ($10 for the 2 days of the course).

If you plan on driving to the course and are interested in purchasing this discounted parking, please let me know for how many days by April 1st. When you arrive, you will have to pay us in cash or by check (made out to MGH) to receive the parking validation sticker(s).

This is very *important*: we cannot wait for checks to be processed by your institution, university, etc. for the price of the parking. You will have to have the check ready on the first day of the course during Registration.

HOW TO DETERMINE HOW MANY STICKERS YOU NEED
Each parking sticker is good for 24 consecutive hours of parking. Once you park in the garage, you cannot take your car out without needing an additional sticker to pay for your re-entry.

For example, if you are driving on the day of the course, leaving at the end of the course that day, and returning the next day - you only need two stickers to pay for those 2 days. If you are arriving in Boston on Sunday at 6pm and leaving at 8am on Wednesday (62 hours), you will need 3 stickers.

If you are unsure of how many you might need, just tell me the maximum amount you would need so I can be sure to have enough stickers.

Thanks,
Allison


Last email before course: (**change link to schedule**)

Subject: FreeSurfer Course Announcement - Final Schedule

Hi everyone,
The FreeSurfer course you all signed up for is upon us. The most updated course schedule can be found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Feb2010CourseSchedule

Please read through the information below.

START TIME
If you signed up for the UNIX Tutorial, it will start at 8am *sharp*. Everyone else should arrive before 9am to register. Please do not walk into the classroom while the UNIX Tutorial is taking place. (Note: The UNIX tutorial is very basic and is meant for those with absolutely no UNIX experience. It is by no means an in depth tutorial and it will not cover scripting. If you changed your mind about attending this tutorial, please let me know. Likewise, the FreeSurfer Jargon talk is aimed at beginners unfamiliar with terms such as surface, volumes, segmentation etc.)

Coffee and a continental breakfast will be served.

PARKING
If you will need to park your car at the Martinos Center, please read the information about Parking on this website:
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Parking

DIRECTIONS
Directions to the course are also located here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Directions

PERSONAL LAPTOPS & DATA
We *cannot* troubleshoot issues that occur when using FreeSurfer on your personal laptop during the tutorial sessions so we ask that you only use the laptops we provide (or have verified ahead of time) for the tutorials. There is an optional session on the first day of the course where we can help you install FreeSurfer and/or run your own data on your personal laptop.

If you are an advanced user and have data you would like to show to us, you may try to do so during the tutorials which have material you have already mastered but keep in mind that we will have to give priority to those working on the tutorial who may have questions.

OPTIONAL INSTALLATION/DATA PROCESSING SESSION **If you have signed up for the FreeSurfer Installation part of the course, you will save a lot of time by downloading the installation file prior to the course. You can do that here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

**If you would like to recon a subject during the "Process Your Own Data" part of the course, be sure to have a laptop with a working version of FreeSurfer installed and the raw scan data (in .dcm, .nii, .mgz) of the subject you wish to launch.

If there are any questions, please feel free to e-mail me.
Allison


Email after course : (**change link to schedule AND survey**)

Thanks very much to everyone for your participation in the FreeSurfer course. I have just a few final announcements and then I promise you won't have to hear from me again!

Some of you have asked where to find the link to the course evaluation. You can find it at the very bottom of this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Oct2010CourseSchedule

Or the direct link (which is rather long and might not be clickable) is:
https://spreadsheets.google.com/viewform?formkey=dHM0ZWFSY0owUVoyQmpMR3NTWUt 2SHc6MA

We do value your feedback and really try to improve each course after hearing your suggestions.

Thanks so much!
Allison

3. Future FreeSurfer Course Ideas

  1. If expand course, consider Larry Wald to cover MRI, Matti to cover MEG, Doug to do Functional
  2. wmparc movie (David)
  3. block diagram for edits
  4. aparc+aseg on talairach
  5. longitudinal analysis
  6. local gyrification index
  7. more info on fmri
  8. From Nick about the tutorial data set: the problem with using these new recons (done with v4.2.0) is that the currently used set, which was done with v4.1.0, and used in the course (ie all the group study stuff), is that that set contains all the edits that sita did. i think it would be best to make our reference buckner40 used for the course based on v4.2.0 though, but i dont know how much effort is involved in transferring edits.}

2011-06-02 10:38