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add comments for Volume.resize() method #80

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Merged
jnolan14 merged 1 commit into from
Jun 29, 2026
Merged

add comments for Volume.resize() method #80

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27 changes: 27 additions & 0 deletions surfa/image/framed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,28 @@ def crop_to_bbox(self, margin=None, crop_like=None):
else:
return self[self.bbox(margin=margin)]


"""
surfa.Volume.resize() and freesurfer MRIupsampledN()/MRIdownsampleN() works differently.

surfa.Volume.resize() logic:
1. keep the original image 'rotation' and 'center' parameters when computing the resampled image geom
2. resampled image crs0 remains the same as originial image. This may cause all voxels to be interpolated
3. force the originial and resampled image in the same RAS space when computing target-source vox2vox matrix
4. by default, 'linear' interpolation method is used

MRIupsampledN()/MRIdownsampleN() logic:
1. the RAS of a voxel is at the center of the voxel, so the image corner is located at CRS = [-.5 -.5 -.5]
2. the center of the resampled image crs0 = -0.5 + 1.0 / (2 * factor) in originial image voxel space (generally used in FS code)
3. the original and resampled images share the same RAS space (implicit)
4. the resampled image p0ras can be computed as p0ras = aff_orig @ crs0
5. re-compute the resampled image 'center' parameters after correcting p0ras of aff_resampled
6. The way the offset/center is set up, some voxels will fall in the same spot as the original volume which means they will not have any interpolation effects.

The target vox2ras from surfa.Volume.resize() and freesurfer MRIupsampledN()/MRIdownsampleN() are different,
but they share the same RAS space. Because the resulting target-source vox2vox is different, surfa.Volume.resize()
interpolates the voxel values from locations that are different from MRIupsampledN()/MRIdownsampleN().
"""
def resize(self, voxsize, method='linear', copy=True):
"""
Reslice image to a specified voxel size.
Expand Down Expand Up @@ -304,6 +326,11 @@ def resize(self, voxsize, method='linear', copy=True):
target_shape = np.asarray(self.geom.voxsize, dtype='float') * baseshape3D / voxsize
target_shape = tuple(np.ceil(target_shape).astype(int))

"""
'target_geom' is computed differently than freesurfer MRIupsampledN()/MRIdownsampleN().
The resulting target-source vox2vox is different. surfa.Volume.resize() interpolates
the voxel values from locations that are different from MRIupsampledN()/MRIdownsampleN()
"""
target_geom = ImageGeometry(
shape=target_shape,
voxsize=voxsize,
Expand Down
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