[Neuroimaging] Slicing images on different planes

[Samuel Botter Martins]

It is clear.

Thank you, Chris.

On Mon, Mar 22, 2021 at 10:07 AM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Hi Samuel,
>
> If the images have come from a single session where multiple scans have
> been taken of the object without removing it from the scanner, and the
> different image sequences you use will induce the same distortions, then
> this should work. In fact, it would not even be necessary to reorient them
> to achieve voxel-to-voxel correspondence.
>
> If the images come from multiple sessions but have been registered so that
> their affines correspond, then yes, resampling should provide
> voxel-to-voxel correspondence. Again, this assumes constant distortion.
>
> If the images have distortions, do not match the above situations, or are
> of unknown provenance, then the odds are good that you'll need to perform
> image registration to bring them into alignment. In most cases, you will
> select an image as canonical and register all other images to that. If
> there is such a thing as a standard reference image, you can also register
> your images to that, which will allow you to use coordinates that others
> can interpret without your image.
>
> As a rule, images with the same expected distortions can be registered
> with a rigid (6 dof) transformation. Registration between modalities with
> different spatial distortions or to a standard reference will generally
> require nonlinear transformations.
>
> If you're just getting started on registration, I would suggest that it's
> worth your time to learn ANTs (https://antsx.github.io/ANTs/). It's
> extremely flexible, but they have a bunch of scripts that handle common
> cases and are useful demonstrations if you need to go beyond them:
> https://github.com/ANTsX/ANTs/tree/master/Scripts. One caveat with ANTs
> is that if there are any shear components to your affine matrix, ANTs will
> not respect them.
>
> Best,
> Chris
>
> ________________________________________
> From: Neuroimaging <neuroimaging-bounces+markiewicz=
> stanford.edu at python.org> on behalf of Samuel Botter Martins <
> sbm.martins at gmail.com>
> Sent: Monday, March 22, 2021 7:53 AM
> To: Neuroimaging analysis in Python
> Subject: Re: [Neuroimaging] Slicing images on different planes
>
> Dear Christopher,
>
>
> On Sat, Mar 20, 2021 at 11:46 PM Christopher Markiewicz <
> markiewicz at stanford.edu<mailto:markiewicz at stanford.edu>> wrote:
> Hi Carl,
>
> It sounds like what you want to do is to interpolate the image in a space
> that's more conveniently rotated so that image dimensions correspond to
> meaningful directions in the world and then visualize slices. The way to go
> about that is going to depend on how well the orientation is described in
> the image affine matrix.
>
> If the affine correctly describes rotations, then you can simply resample
> the image with nibabel.processing.resample_to_output() (
> https://nipy.org/nibabel/reference/nibabel.processing.html#resample-to-output).
> That will produce an image in-memory that you can work with as you show in
> your code, or save and open in another viewer.
>
> So, does this mean I could reorient/serialize all images in memory to the
> same voxel space?
> I mean, regardless of the orientation of each image stored on file, this
> function will reorient all of them to the same voxel coordinate space, so
> that a voxel img[x, y, z] correspond to the precise position in all images,
> am I correct?
> Of course, if the image has stored its affine matrix.
>
> Best.
>
> --
> Prof. Dr. Samuel Botter Martins
> Professor in Federal Institute of Education, Science and Technology of São
> Paulo
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>


-- 
*Prof. Dr. Samuel Botter Martins*
Professor in Federal Institute of Education, Science and Technology of São
Paulo
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