we use a procedure from Avi Snyder to compute (but not apply) a 12 degree
of freedom transform to MNI space. This is available for coordinate
reporting and we use it a bit for things like finding the approximate
center of the brain
cheers
Bruce
On Wed, 19 Aug 2015, chenhf_uestc wrote:
Hi, Bruce Thanks for your reply. Another question is What is talairach
transformationprocedure (This computes the affine transform from the orig volume to the M
NI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer scrip
t called talairach). Why I need to transform from native space to MNI305
(We perform recon-all in the native space)? Best, Feng
____________________________________________________________________________
发件人：Bruce Fischl <fis...@nmr.mgh.harvard.edu>
发送时间：2015-08-18 22:09
主题：Re: [Freesurfer] Query about transformations in the recon-all
收件人："Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
抄送：
Hi Feng
we compute many transforms for many reasons. The em reg is computed once
in the image with skull to help with skull stripping, then again to the GCA
atlas to initialize the nonlinear transform for computing the aseg
segmentation.
cheers
Bruce
On Tue, 18 Aug 2015, chenhf_uestc wrote:
> Dear Freesurfer experts,
>
> I have some questions in the recon-all. After reading online manual and d
iscussing 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 t
o the MNI305 atlas using the
> MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer scr
ipt called talairach), why I
> need transform from native space to MNI305; 2. EM (GCA) Registration (Com
putes transform to align the
> mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/avera
ge). What is the GCA atlas?
> what is the usage of this atlas? 3. CA Register (Computes a nonlinear tra
nsform 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) Registr
ation (Affine? 12 dof?); 4.
> EM Registration, with Skull (Computes transform to align volume mri/nu_no
neck.mgz with GCA volume
> possessing the skull);
>
> Is there any detailed documentation in the online manual to introduce the
se transformation? Could
> anyone give me a website?
>
> Any help would be greatly appreciate.
>
> Best,
> Feng
>
>
>
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