Not same coordinates displayed into registered files

Questions about Anatomist manipulation

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pron.a
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Not same coordinates displayed into registered files

Postby pron.a » Mon Jan 29, 2018 10:18 am

Dear Anatomist community,

I am not sure this topic really belong to Anatomist section specifically but it seems the closest section to post into.
Here is a description of what I encounter:

I have two niftii volumes produced by the HCP consortium, a T1 data and the associated diffusion data. According to HCP description paper and scripts
diffusion data is registered into the T1 space (T1 itself has been rigidly registered to MNI_152 space in a previous step).

When I load both volumes into Anatomist and load their referential I observe indeed that both volumes have a transformation toward common MNI space.
When I display data in the common referential, both volumes seems to be aligned. However when I look at the mm coordinates into the MNI space of the linked cursor it does not have the same exact coordinates in both images (see captures enclosed). In addition, I noticed that the difference seems to be in coordinate axis corresponding to the displayed axis (see captures enclosed). Since I want to put meshes from T1 into the diffusion referential I need
the coordinates to correspond.

So wondering if it was only a display problem or a registration problems (only one coordinate is wrong because other may be fixed due to selected view) I checked for affines using nibabel and regarding the affines in seems volumes are well aligned. So I verified affine display into anatomist (the aims_mm to mni_mm affine) by recomputing it using numpy and checking that I obtain well the nibabel affine in the end. Calculation seems to be accurate.

Then using the different transformations I checked if going from a voxel into T1 data I would obtain exactly a voxel into diffusion data (the python script is enclosed)

What I see is that I have a small shift on the last two coordinates. I don't know if it is an error of estimation of the aims_mm to ras_mm, a weird bug
or something I misunderstand in coordinates system.

If you have any hint :P

Alex

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riviere
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Re: Not same coordinates displayed into registered files

Postby riviere » Mon Jan 29, 2018 10:29 am

Hi,
It seems that you forgot to attach the images :)
I'm not totally sure to understand your problem then. But I have perhaps a beginning of clue: When Anatomist displays volumes, the volume slice position is snapped to the center of the slice, depending on the volume voxel size. So if you display two volumes in two different windows, even if they are in correspondence through coordinates transformation, the position may differ a bit due to the slice position.
Could this be the answer of your question ?
Denis

pron.a
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Joined: Mon Feb 22, 2016 10:09 am

Re: Not same coordinates displayed into registered files

Postby pron.a » Mon Jan 29, 2018 12:04 pm

Hello Denis,
thank you so much for your answer. oups sorry about that. I had a warning message when trying to upload the files but I tought it was ok :( Actually interface is telling me the files are too eavy (500kb).
Yes definetly ! But I was not sure either it was just display in the slice or real registration error. I put a link towards files so that you can make yourself an idea :)
https://cloud.int.univ-amu.fr/index.php ... 6ALLQBQPXP

Have a good day

Alex

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riviere
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Re: Not same coordinates displayed into registered files

Postby riviere » Mon Jan 29, 2018 12:37 pm

I cannot be completely sure without actually manipulating the data but I think it's actually the "snap to slice" of anatomist which disturbs you. It's just that the position of the cursor is snapped to match the (integer) slice number displayed on the slice cursor, the data and its registration should be OK.
Denis

pron.a
Posts: 22
Joined: Mon Feb 22, 2016 10:09 am

Re: Not same coordinates displayed into registered files

Postby pron.a » Mon Jan 29, 2018 1:49 pm

Ok super ! Thank you very much Denis :)


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