Load vol file into 3D Slicer from Morita machine

Hi,

I have a volume file named *.vol from Morita machine. I am trying to convert it into a stl or obj file. It is not supported to be loaded by 3D Slicer right now. Is there any extension available? Or any other way to do it like a matlab script? Thanks in advance.

Is there an option to export the volume in DICOM format?
Can you share an example .vol file?

Hi Andras,

Thanks for your reply. The .vol file can be only opened by a software named OneVolumeViewer form Morita. I have uploaded the .vol file and the software.

https://drive.google.com/open?id=1iABWN3jzvWv7PNrMhFKZhQRxD9KyGqgV

I’m not sure it’s the same file type (.vol may be an overused file extension) but here’s some code to read a .vol file from a microCT machine:

This .vol file has a human-readable header. From that you can determine image geometry (size, spacing, origin) and write it to a header file. You can then open that file in Slicer.

For example, here is the header for the file you shared:

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: short
dimension: 3
space: left-posterior-superior
sizes: 504 501 500
space directions: (0.08,0,0) (0,0.08,0) (0,0,0.08)
kinds: domain domain domain
endian: little
encoding: raw
space origin: (0,0,0)
byte skip: 800
data file: CT_0.vol

If you save the content above to a file named CT_0.nhdr (or download it from here) then you can open that file in Slicer.

image

Hi Andras,

This really helps! I do appreciate it.

Hi Andras,

I have successfully loaded the vol file, but the rendering result is different from yours. (It looks incorrectly) Is there any steps before volume rendering? Thanks for your help.

Voxels values of the scan are uncalibrated, it is not in Hounsfield units but in tens of thousands range. So, you need to adjust the transfer functions accordingly (you need to open Advanced section and drag points outside the current default range, which are specified for Hounsfield units).

Hi Andras,

Here is my result. I was trying but failed to achieve the result similar to yours.
image
Could you tell the details what configuration you were using for the above one you posted? Screenshots are the best if you could attach. Thank you for your time and effort.

Hi,

I am confusing about the Hounsfield units. I watched several tutorals but they skip the step. Where and how can I modify this Hounsfield units or transfer functions configuration? Thanks for the help.

I had to tune the transfer functions, which were not easy, because the points were way out of normal CT range. I would recommend to rescale voxel intensities using SimpleFilters module:

image

After this you can use built-in volume rendering presets, such as “CT-AAA2” or “CT-Cardiac3”, and move “Shift” slider to fine-tune what is displayed.