Hi Ping
we don't apply the linear registration to any image - we use it to
initialize the nonlinear warp. And yes, the nonlinear warp is stored as a
128^3 array with 2 voxel spacing and interpolation between them. You can
visualize the .m3z directly in freeview as a 3-frame displacement volume
or mri_convert it I believe.
cheers
Bruce
On Thu, 29 Aug 2019, ping cao wrote:
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Dear Tim,
Thank you for your reply!
1) I want the the deformation field is the displacement from the template
image to the linearly-aligned image defined.
2) I just use the recon-all to generate the file.
3) What I want is to first linearly register to template to obtain a linearly
registered image, and then perform nonlinear registration to obtain the
deformation field from the origin image to the template.
I don't know which image is linearly registered in freesurfer, which one is
after nonlinear registration, and the deformation field file is
128*128*128*3, I can't think of it as displacement I want .
Best,
ping
Tim Schäfer <ts...@rcmd.org> 于2019年8月28日周三 下午4:30写道：
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Could you explain what you are trying to achieve and which
transformation you are referring to? I don't get:
1) what are the input and output files of the registration for
which you want the deformation field?
2) What command did you use to perform the registration?
3) Is it linear or nonlinear?
(The file <subject>/mri/transforms/talairach.m3z stores a
transformation field of a nonlinear registration, but I'm not
sure whether it is what you want.)
I find the quoted part a bit confusing (but that may just be me).
The first sentence talks about nonlinear registration, and the
others talk about linear registration -- but still mention a
deformation field. Maybe some more context would help.
For a linear registration, an affine matrix should be all you
need.
Tim
> On August 28, 2019 at 9:55 AM ping cao <pingcao...@gmail.com>
wrote:
>
>
> External Email - Use Caution
>
> Dear expert，
>
> I saw a paper mentioned this ：
>
> By using the *deformation field* from nonlinear registration,
we can
> > build the correspondence between voxels in the template and
each
> > linearly-aligned image. For instance, for each voxel (x, y,
z) in the
> > template image, we can find its corresponding voxel (x + dx,
y + dy, z +
> > dz) in each linearly-aligned image, where (dx, dy, dz) is the
> > *displacement* from the template image to the
linearly-aligned image
> > defined by the deformation field.
>
>
>
> So, I want to get the deformation field from the template to
the linearly
> registered image(flirt_T1).
>
> Can Freesurfer do this? Which file is a linearly registered
image that
> does not contain an affine transformation? How can I get this
deformation
> field?
>
>
> Your help is greatly appreciated.
>
>
> Best,
> ping
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Forschung - Klinische Bildgebung
Klinik für Psychiatrie, Psychosomatik und Psychotherapie des
Kindes- und Jugendalters
Universitätsklinikum Frankfurt / Haus 93, Raum A 305
Deutschordenstr. 50, 60528 Frankfurt am Main
Tel.: +49 (0)69 6301 85832
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