# Load vol file into 3D Slicer from Morita machine

**URL:** <https://discourse.slicer.org/t/load-vol-file-into-3d-slicer-from-morita-machine/4815>\
**Category:** Support\
**Created:** [November 20, 2018, 2:44pm UTC](https://discourse.slicer.org/t/load-vol-file-into-3d-slicer-from-morita-machine/4815 "2018-11-20T14:44:52Z")\
**Posts on this page:** 1\
**Showing post:** 15

<div class="post-metadata">

**Author:** ![Alexander\_Shiryaev](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_shiryaev/32/81512_2.png) [@Alexander\_Shiryaev](https://discourse.slicer.org/u/Alexander_Shiryaev)\
**Post date:** [December 1, 2025, 5:06am UTC](https://discourse.slicer.org/t/load-vol-file-into-3d-slicer-from-morita-machine/4815/15 "2025-12-01T05:06:07Z")

</div>

# Instruction to Create `.nhdr` file

Use the following template for your `.nhdr` file:

```auto
NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: signed short
dimension: 3
space: left-posterior-superior
sizes: Z Y X
space directions: (0,0,S) (S,0,0) (0,S,0)
kinds: domain domain domain
endian: little
encoding: raw
space origin: (0,0,0)
byte skip: B
data file: CT_0.vol

```

You need to fill values from your `.vol` header:  
`X`, `Y`, `Z`, `S`, `B`

## Voxel size (`S`)

Look for the grid size in the `.vol` XML header, e.g.:

```xml
<tfXGridSize value="0.125"/>
<tfYGridSize value="0.125"/>
<tfZGridSize value="0.125"/>

```

⇒ `S` = 0.125

## Dimensions (`X`, `Y`, `Z`)

Check the minimum and maximum indices:

```xml
<FYI>
  <XMin value="-352"/>
  <XMax value="352"/>
  <YMin value="-352"/>
  <YMax value="352"/>
  <ZMin value="-162"/>
  <ZMax value="161"/>
  ..
</FYI>

```

`X` = `XMax` - `XMin` + 1 = 352 - (-352) + 1 = 705  
`Y` = `YMax` - `YMin` + 1 = 352 - (-352) + 1 = 705  
`Z` = `ZMax` - `ZMin` + 1 = 161 - (-162) + 1 = 324

## Byte skip (`B`)

total voxels = `X` \* `Y` \* `Z` = 161036100  
voxel size = 2 bytes (because data type in `.vol` is 16-bit integer)  
raw data size = total voxels \* voxel size = 322072200 (bytes)

Raw data located at the very end of the `.vol` file, so the byte skip parameter can be calculated as:  
`B` = total `.vol` file size - raw data size

## Adjust axes (if necessary)

If after import the axes look incorrect, modify the `space directions` line, for example:

```auto
space directions: (S,0,0) (0,S,0) (0,0,S)

```

Test different permutations until the orientation matches your viewer.

## Data type consideration

Use `signed short` data type, not `unsigned short`, because in your `.vol`:

- `0x8000` value corresponds to _void_
- and all other values correspond to actual intensities

## Python parser for reference

```py
import struct, tempfile, subprocess
import numpy as np

def load_data (path: str, dtype = np.int16, extract_header: bool = False) -> np.ndarray:
    with open(path, 'rb') as f:
        n = struct.unpack("<I", f.read(4))[0]
        data = f.read(n)
        assert data.decode('ascii') == "JmVolumeVersion=1"

        # XML
        n = struct.unpack("<I", f.read(4))[0]
        data = f.read(n)
        if extract_header:
            with tempfile.NamedTemporaryFile() as fht:
                fht.write(data)
                fht.flush()
                subprocess.run(["xmllint", "--format", "--output", path + ".header.xml", fht.name])

        n = struct.unpack("<I", f.read(4))[0]
        data = f.read(n)
        assert data.decode('ascii') == "CArray3D"

        # X limits
        x_min, x_max = struct.unpack("<ii", f.read(8))
        X = x_max - x_min + 1

        # Y limits
        y_min, y_max = struct.unpack("<ii", f.read(8))
        Y = y_max - y_min + 1

        # Z limits
        z_min, z_max = struct.unpack("<ii", f.read(8))
        Z = z_max - z_min + 1

        print(f"X={X} Y={Y} Z={Z}")

        # voxels
        d = np.frombuffer(f.read(), dtype=dtype)
        print(len(d))
        assert len(d) == X * Y * Z
        d = d.reshape((X, Y, Z))
        return d

```

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