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| == Reading == Information on spherical registration [[http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates|here]]. |
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| == Homework == | Please note that this course caters for users with no FreeSurfer experience whatsoever. If you are a complete beginner and would like to gain some foundation in working/interacting with FreeSurfer, then these resources can be useful to you but are not necessary to complete before you arrive at the course. However, we strongly recommend attempting to work with Unix before the course so that you feel comfortable with the pace on the first day, even though we will cover an introduction to Unix in the very first talk. |
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| == COURSE MATERIALS == | |
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| == Explanation == the phrase "put something in a different space' can also be used for reslicing. Applying a transform is more. For example 'map to Talairach space" means that the brain is rotated, translated, and even stretched first to fit the talairach average and then resliced. So its position and even shape/size is changed by a transform and then the reslicing happens according to whatever 'camera settings' are used. |
'''UNIX'''<<BR>> If you are unfamiliar with UNIX, it may help to do this online tutorial: <<BR>> http://www.ee.surrey.ac.uk/Teaching/Unix/ |
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| So applying a transform means: 1. undo camera setting of source -> 2. apply geometric transform (rotation, translation, strecthing, shearing) -> 3. use camera setting of target (or the same as source again whatever the user wants). |
Other good UNIX references are: <<BR>> http://www.fmrib.ox.ac.uk/fslcourse/unix_intro/ <<BR>> http://docstore.mik.ua/orelly/linux/lnut/index.htm <<BR>> https://www.codecademy.com/courses/learn-the-command-line |
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| For reslicing you do not have step 2. | '''SCRIPTING'''<<BR>> Scripting will not be covered during the course, but the following are some good references:<<BR>> http://www.linuxjournal.com/article/1299 <<BR>> https://supportweb.cs.bham.ac.uk/documentation/tutorials/docsystem/build/tutorials/unixscripting/unixscripting.html |
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| The camera setting can be understood as for example distance between slices (voxel size), position and orientation of slices. It usually also includes the data type (eg. int, float...). These settings are stored in each mgz file and also referred to as the 'geometry'. |
'''MR'''<<BR>> If you are unfamiliar with MR physics, you can read up on it here: <<BR>> http://www.cis.rit.edu/htbooks/mri/ There will be an optional talk that will go over the basics of MR physics. '''FREESURFER RELATED'''<<BR>> This document was put together by a member of the FreeSurfer lab, which details some fundamental information and jargon which you may find useful when learning FreeSurfer for the first time. Download and read the following word document: [[attachment:FS_homework_doc]]. We have two new videos to help you familiarize yourself with working in FreeSurfer or Freeview: <<BR>> 1. Qualtiy Checking a Recon: https://www.youtube.com/watch?v=AR83_Bt04VQ <<BR>> 2. Freeview Demo: https://www.youtube.com/watch?v=Mv-ECowxq2o 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: <<BR>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Not all of the slides are up or updated yet, but feel free to look at what is there. You can also find videos of the course lectures here: <<BR>> http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA You can read up on the techniques and applications of FreeSurfer here (found under the References section): <<BR>> https://surfer.nmr.mgh.harvard.edu/fswiki/ You can download FreeSurfer and process your own data. Instructions on installation are here: <<BR>> https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall |
How to Prepare for the FreeSurfer Course
Please note that this course caters for users with no FreeSurfer experience whatsoever. If you are a complete beginner and would like to gain some foundation in working/interacting with FreeSurfer, then these resources can be useful to you but are not necessary to complete before you arrive at the course. However, we strongly recommend attempting to work with Unix before the course so that you feel comfortable with the pace on the first day, even though we will cover an introduction to Unix in the very first talk.
COURSE MATERIALS
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
https://www.codecademy.com/courses/learn-the-command-line
SCRIPTING
Scripting will not be covered during the course, but the 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/
There will be an optional talk that will go over the basics of MR physics.
FREESURFER RELATED
This document was put together by a member of the FreeSurfer lab, which details some fundamental information and jargon which you may find useful when learning FreeSurfer for the first time. Download and read the following word document: FS_homework_doc.
We have two new videos to help you familiarize yourself with working in FreeSurfer or Freeview:
Qualtiy Checking a Recon: https://www.youtube.com/watch?v=AR83_Bt04VQ
Freeview Demo: https://www.youtube.com/watch?v=Mv-ECowxq2o
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
Not all of the slides are up or updated yet, but feel free to look at what is there.
You can also find videos of the course lectures here:
http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA
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/QuickInstall