[Mristudio-users] spatial normalization

[susumu mori]

This is a good question.

> You can perform fiber tracking in the native MRI space. Here "native"
means the MRI data as they were acquired.
> You can also perform fiber tracking after you standardized the MRI data in
the standard coordinate.
>> The standardization is either by linear or non-linear transformation. For
the linear, you can use rigid (just relocate the brain to a standard
position and orientation without changing the shape) or affine (you can
adjust the brain size and shape too).
>> To perform fiber tracking after the standardization, you have to
standardize the tensor file, not FA or vector file. You'd better standardize
the tensor file, then create new FA and vector maps from the standardized
tensor because standardization of a vector field is difficult.
>> After standardization, you can expect ROI drawing could be more
reproducible. For example, if you want to identify the anterior limb of
internal capsule for fiber tracking, you can create a protocol like, "draw
ROI on the internal capsule at coronal slice #50". This kind of protocol is
not applicable if we use the native space.
>> Also, standardization often involves interpolation to finer resolution
(say 2.5 mm native resolution to 1 mm standard coordinates). This has some
impact on fiber tracking. I believe the fiber-angle threshold (this prevents
sharp turning angle) is effectively reduced. So, you may obtain longer
uninterrupted streamlines. Cosmetically, the tracking results may look
better with finer resolution.
>> Drawback is, because of the extra standardization step that involves
interpolation, blurring, tensor re-orientation, and other issues, you may
invite some questions and criticisms.

In my personal opinion, it is not an issue of one is better than the other.
You need to decide the way you do the study and stick to it. I personally
support the standardized approach.

Susumu

2010/1/17 yan hao <hao_y at hsc.pku.edu.cn>

> Hi all,
> I wonder if I need to do spatial normalization before I do the fiber
> tracking. I know I can do this in the original space. However some fibers
> are not easy to define in the original space, so if the images are all in a
> standard space, I can draw a ROI in a certain slice of the brain.If the
> spatial normalization is acceptable, could you suggest the way to do the
> spatial normalization？Any help is highly appreciated.
> Best,Hao_______________________________________________Mristudio-users
> mailing listMristudio-users at mristudio.orghttp://
> lists.mristudio.org/mailman/listinfo/Unsubscribe, send a blank email to:
> Mristudio-users-unsubscribe at mristudio.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100120/86df7d68/attachment.html