# Copy headers / metadata between segmentations of different resolutions

**URL:** https://discourse.itk.org/t/copy-headers-metadata-between-segmentations-of-different-resolutions/6558
**Category:** Algorithms
**Tags:** python, segmentation, nrrd, simpleitk
**Created:** [April 9, 2024, 4:23pm UTC](https://discourse.itk.org/t/copy-headers-metadata-between-segmentations-of-different-resolutions/6558 "2024-04-09T16:23:52Z")
**Posts on this page:** 2
**Page:** 1

<div class="post-metadata">

### Author: ![Cristobal\_Rodero](https://discourse.itk.org/user_avatar/discourse.itk.org/cristobal_rodero/32/3615_2.png) [@Cristobal\_Rodero](https://discourse.itk.org/u/Cristobal_Rodero)
#### Post date: [April 9, 2024, 4:23pm UTC](https://discourse.itk.org/t/copy-headers-metadata-between-segmentations-of-different-resolutions/6558/1 "2024-04-09T16:23:53Z")

</div>

I have a coarse segmentation that I smooth, and the smoothing techniques overwrites the header. I want to retrieve the original one but I have had no success so far. The headers are

```auto
_, coarse_header = nrrd.read(path_to_coarse_image)
smooth_image, smooth_header = nrrd.read(path_to_smooth_image)

```

coarse\_header:

```auto
OrderedDict([('type', 'short'),
             ('dimension', 3),
             ('space', 'left-posterior-superior'),
             ('sizes', array([748, 749, 749])),
             ('space directions',
              array([[0.26375667, -0.09178596, -0.1095799],
                     [0.10153998, 0.2821788 , 0.00804705],
                     [0.10060839, -0.04416401, 0.27915496]])),
             ('kinds', ['domain', 'domain', 'domain']),
             ('endian', 'little'),
             ('encoding', 'raw'),
             ('space origin',
              array([-148.47837839, -45.81777566, -68.16309759]))])

```

smooth\_header:

```auto
OrderedDict([('type', 'uint8'),
             ('dimension', 3),
             ('sizes', array([1314, 884, 900])),
             ('encoding', 'raw'),
             ('spacings', array([0.15, 0.15, 0.15])),
             ('axis mins',
              array([-139.14450073, -3.77869463, -26.14629364]))])

```

Now I don’t care about the information in the smooth\_header. The main difference is that it has a higher resolution now, from a voxel spacing of 0.3 now is 0.15.

I figured that the spacing information of the coarse\_header is encoded in the norm of the vectors of `space_directions`, so I copied the the header as follows:

```auto
new_smooth_header = dict(coarse_header)

#Update the fields in the new header to match the coarse header, except for the spacing
new_smooth_header['sizes'] = smooth_header['sizes']

smooth_spacing = np.array(smooth_header['spacings']) # Spacing from smooth_header
coarse_space_directions = np.array(coarse_header['space directions']) # Space directions from coarse_header

# Calculate new space directions for smooth header
new_smooth_space_directions = np.copy(coarse_space_directions)
for i in range(len(smooth_spacing)):
    norm_coarse = np.linalg.norm(coarse_space_directions[i])
    new_smooth_space_directions[i] = smooth_spacing[i] * (coarse_space_directions[i] / norm_coarse)

new_smooth_header['space directions'] = new_smooth_space_directions

# # Assign the new header to the smooth image
# smooth_image_with_coarse_header = (smooth_image, new_smooth_header)

ordered_new_smooth_header = OrderedDict(new_smooth_header.items())

nrrd.write(path_to_save_image, smooth_image, header=ordered_new_smooth_header)

```

Now the new header is

```auto
OrderedDict([('type', 'uint8'),
             ('dimension', 3),
             ('space', 'left-posterior-superior'),
             ('sizes', array([1314, 884, 900])),
             ('space directions',
              array([[0.13187834, -0.04589298, -0.05478995],
                     [0.05076999, 0.1410894 , 0.00402352],
                     [0.0503042 , -0.02208201, 0.13957748]])),
             ('kinds', ['domain', 'domain', 'domain']),
             ('encoding', 'raw'),
             ('space origin',
              array([-148.47837839, -45.81777566, -68.16309759]))])

```

So _in theory_ they should be in the same space, as far as I understand. They’re not. Size seems fine, as well as orientation, it looks that it just need a translation, but I don’t know which one.

 ![header_problems](https://discourse.itk.org/uploads/default/original/2X/7/7863373698f7d496970efd29d5ba17de2bfb1157.jpeg)

---

<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [April 9, 2024, 7:28pm UTC](https://discourse.itk.org/t/copy-headers-metadata-between-segmentations-of-different-resolutions/6558/2 "2024-04-09T19:28:37Z")

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How does the smooth image look like if you don’t fiddle with its header? You seem to be ignoring the origin in the smooth image (`axis mins` field), maybe you shouldn’t, or you need to use it somehow? The smooth image also has identity orientation, maybe you need to preserve that?

What is lacking is information how your smooth image was produced. That information is needed, to account for its spatial discrepancy (if any).