I have done a registration in the general registration module (BRAINS) but the output image volume does not match with the fixed image volume. The goal is to apply a linear transformation (rotation and translation) to a CT dicom volume and then save the transformed volume as dicom. As you can see, I have imported the CT dicom volume (fix_img) and I have cloned it (mov_img).
In the Transform module I have created a new linear transform,
I have moved the fix_img under Transformed
and then I have rotated and translated the volume.
As you can see in the image below, I created a transform matrix with different rotations and translations. Strangely, unlike the translations, the rotations of the planes seem set to 0° despite being present in the Transform matrix. In other words, for example if I rotate the LR plane of 20° and then rotate the IS plane of 10°, then the rotation of the LR plane will be shown at 0°. I don’t know if this will affect the final result in any way.
Then I have applied the transformations to the fix_img using Harden transform.
In the general registration (BRAINS) module, I have set as Fixed Image volume the fix_img and as Moving Image volume the mov_img that will be transformed into the fixed image space using the linear transformation.
Unfortunately, Output image volume is not properly rotated and translated.
Another strange thing I have noticed is that if I go back to Data and display the fix_img volume, it doesn’t seem rotated and translated even though I have used harden transform. If I re-apply the linear transformation to the fix_img volume it is correctly rotated and moved. But this should not happen as I have already applied the linear transformation using harden transform. It is as if selecting a volume in Data, each transformation is deleted.
Does anyone know how to save a dicom volume with a new reference system after a linear transformation?