|
Size: 1184
Comment:
|
Size: 2667
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| == Reading == Information on spherical registration [[http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates|here]]. |
|
| Line 5: | Line 3: |
| == Homework == | == "Required" Readings == If you are a beginner to !FreeSurfer, the following content is HIGHLY recommended to enhance your enjoyment of the course. 1. Please view this video introducing you to interacting with !FreeSurfer through Unix: -Link Coming Soon- 2. Please familiarize yourself with the terms in this glossary: https://docs.google.com/document/d/1x6PsE6tlOXF7zcvkhwTGngD_B8Mslzsvzlo6_alP_28/edit?usp=sharing |
| Line 8: | Line 12: |
| == 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. |
_____ |
| Line 16: | Line 14: |
| 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). |
== Bonus Course Materials == |
| Line 21: | Line 16: |
| For reslicing you do not have step 2. | '''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/ |
| Line 23: | Line 20: |
| 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'. |
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 '''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 '''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. Quality 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
"Required" Readings
If you are a beginner to FreeSurfer, the following content is HIGHLY recommended to enhance your enjoyment of the course.
Please view this video introducing you to interacting with FreeSurfer through Unix: -Link Coming Soon-
Please familiarize yourself with the terms in this glossary: https://docs.google.com/document/d/1x6PsE6tlOXF7zcvkhwTGngD_B8Mslzsvzlo6_alP_28/edit?usp=sharing
_
Bonus 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:
Quality 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