I have two volumes and I want to overlay them. However, as seen in the image, they do not perfectly overlay. I have set their origins to be the same, aligned their directions from IJK to RAS, adjusted their spacing values, dimensions, and affine matrices to be identical. Despite all these adjustments, they still do not overlay properly. What other parameters can I change to achieve this?
Please copy here the complete image header of both images.
this one is my volume:
Image (0x7f7e26737340)
RTTI typeinfo: itk::Image<short, 3u>
Reference Count: 1
Modified Time: 12445
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 12422
UpdateMTime: 12444
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 256]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 256]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 256]
Spacing: [0.2, 0.2, 0.2]
Origin: [53.5598, 27.6676, -19.3769]
Direction:
-0.84309 -0.149155 -0.516674
-0.122292 -0.88242 0.454291
-0.523683 0.446193 0.725719
IndexToPointMatrix:
-0.168618 -0.029831 -0.103335
-0.0244584 -0.176484 0.0908582
-0.104737 0.0892386 0.145144
PointToIndexMatrix:
-4.21545 -0.61146 -2.61841
-0.745774 -4.4121 2.23097
-2.58337 2.27145 3.62859
Inverse Direction:
-0.84309 -0.122292 -0.523683
-0.149155 -0.88242 0.446193
-0.516674 0.454291 0.725719
PixelContainer:
ImportImageContainer (0x600006145920)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, short>
Reference Count: 1
Modified Time: 12441
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f7dceae0000
Container manages memory: true
Size: 16777216
Capacity: 16777216
and this one is original:
Image (0x7f7df6974590)
RTTI typeinfo: itk::Image<short, 3u>
Reference Count: 1
Modified Time: 8217
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 8194
UpdateMTime: 8216
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 256]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 256]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 256]
Spacing: [0.2, 0.2, 0.2]
Origin: [53.5598, 27.6676, -19.3769]
Direction:
-0.84309 -0.149155 -0.516674
-0.122292 -0.88242 0.454291
-0.523683 0.446193 0.725719
IndexToPointMatrix:
-0.168618 -0.029831 -0.103335
-0.0244584 -0.176484 0.0908582
-0.104737 0.0892386 0.145144
PointToIndexMatrix:
-4.21545 -0.61146 -2.61841
-0.745774 -4.4121 2.23097
-2.58337 2.27145 3.62859
Inverse Direction:
-0.84309 -0.122292 -0.523683
-0.149155 -0.88242 0.446193
-0.516674 0.454291 0.725719
PixelContainer:
ImportImageContainer (0x600006179440)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, short>
Reference Count: 1
Modified Time: 8213
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f7e52000000
Container manages memory: true
Size: 16777216
Capacity: 16777216
there is two volume: example_nii - Google Drive
Nifti file stores image orientation in a redundant and potentially ambiguous way, so this kind of issues are practically inevitable. I would recommend to use nrrd file format instead.
