• CoursePrep

How to Prepare for the FreeSurfer Course

Reading

Information on spherical registration here.

Homework

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.

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).

For reslicing you do not have step 2.

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'.