Dear Freesurfer experts,
I have some questions in the recon-all. After reading online manual and
discussing with the experts in the maillist, I have known all the recon-all
procedures performed in the individual native space. However, I very confuse
that there are many transformations in the recon-all, e.g., 1. talairach
transformation (This computes the affine transform from the orig volume to the
MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through
a FreeSurfer script called talairach), why I need transform from native space
to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz
volume to the default GCA atlas found in FREESURFER_HOME/average). What is the
GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a
nonlinear transform to align with GCA atlas. Creates the file
mri/transform/talairach.m3z). Why we should align with GCA atlas? This
transform is nonlinear, and what is the transform in the EM (GCA) Registration
(Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align
volume mri/nu_noneck.mgz with GCA volume possessing the skull);
Is there any detailed documentation in the online manual to introduce these
transformation? Could anyone give me a website?
Any help would be greatly appreciate.
Best,
Feng
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