Dear Konstantinos,
Your error is quite weird. If you make some calculation it turns out that the origin is the same in both cases (136 or 121 with flipped dimension on a 256 pixel image). Something's weird is going on.
If you open them with check_reg do they look ok?
Furthermore, if you read the volumes at the low level (don't know the right term), are they already matched at the pixel size?
Can you triple check the whole pipeline for some trivial errors maybe? (I don't know... maybe some input images wrong, deformation field not chosen correctly...).
I hope some experts can chime in concerning the orientation issue, as you're getting the right bounding box and everything but wrong pixel orientation...
Regards
Luca
-----Original Message-----
From: SPM (Statistical Parametric Mapping) <[log in to unmask]> On Behalf Of Konstantinos C
Sent: 07 June 2020 15:32
To: [log in to unmask]
Subject: Re: [SPM] Origin - normalisation - SPM12
Dear Luca,
Thanks for your reply.
The native MRI 01_1_mr.nii has dimensions 256x220x256, Vox size 0.977x0.8x0.977, origin 121 145 150.
I perform the segmentation with default settings except from enabling to save the deformation fields.
Then I go to "normalise write" and add the deformation field iy_01_1_mr.nii and as image to write I add for example the MNI template avg152T1.nii. Then as bounding box I add [NaN NaN NaN; NaN NaN NaN] and as a voxel size [NaN NaN NaN], although it is not 100% accurate in this example I use the nearest neighbor interpolation (the actual images that I normalise are atlases).
The result is the wavg152T1.nii, which has dimensions 256x220x256, Vox size -0.977x0.8x0.977, origin 136 145 150.
As you can observe the result is suboptimal. The dimensions are the same but the origin is off and the Vox size is not the same given the negative sign in one dimension.
If I do another reslice with the mri defining the space I get the correct origin and voxel size but is it needed to do a reslice after a normalization?
Am I doing something totally wrong?
Cheers,
Konstantinos
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