# How can I create dcm (or mesh) files from .vol and vgi files and .raw?

**URL:** <https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346>\
**Category:** Support\
**Created:** [May 23, 2024, 12:34pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346 "2024-05-23T12:34:09Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![CatherineBone](https://avatars.discourse-cdn.com/v4/letter/c/f19dbf/32.png) [@CatherineBone](https://discourse.slicer.org/u/CatherineBone)\
**Post date:** [May 23, 2024, 12:34pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/1 "2024-05-23T12:34:09Z")

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Hi, I’ve been given two files that contain the CT scans of two Neanderthal  
The first one contains a .vgi and a .vol and the second a .raw  
I need to create dicom files from the .vol files and .raw files that I can create mesh files (obj or stl) from. Or skip the dicome files part and go straight to mesh files.

I’ve downloaded and installed the slicermorph and Raw Image Guess extentions but can’t seem to get any useable data out.

For the .vol data - I load it in using the Raw Image Guess module - tried to enter in the size of the xyz dimentions from the .vgi file but the sliders dont go up that high, and I tried a tutorial online ([https://youtu.be/ajpOQEAyWkA?si=BoqaenOgTG2fNF8f](https://youtu.be/ajpOQEAyWkA?si=BoqaenOgTG2fNF8f)) but im just getting lots of fuzziness!  
This is the .vgi file:  
{volume1}  
[representation]  
size = 1374 1401 2000  
mirror = 0 0 0 0  
resamplemode = not activated  
datatype = unsigned integer  
datarange = 0 65535  
bitsperelement = 16  
[file1]  
RegionOfInterestStart = 0 0 0  
RegionOfInterestEnd = 1373 1400 1999  
FileFormat = raw  
Size = 1374 1401 2000  
Name = LB\_BH1\_01.vol  
Datatype = float  
datarange = -94.1933 394.005  
BitsPerElement = 32  
{volumeprimitive1}  
[section1]  
min = 0  
max = 65535  
offset = 0  
name = section [0]

[geometry]  
status = visible  
relativeposition = 0 0 0  
position = 10.5004 -38.0008 0  
resolution = 0.1271 0.1271 0.1271  
scale = 1 1 1  
center = 687 700.5 1000  
rotate = 1 0 0 0 1 0 0 0 1  
unit = mm  
[volume]  
volume = volume1  
[description]  
text = LB\_BH1\_\_  
[segment1]  
status = activated  
description = 0  
opacityx = 0 12644 65535  
redx = 0 65535  
greenx = 0 65535  
bluex = 0 65535  
opacityvalue = 0 0 2  
redvalue = 255 255  
greenvalue = 255 255  
bluevalue = 255 255  
{default}  
[version]  
release = VGStudioMax 1.2.1 (build 352)  
{scene}  
[viewer]  
perspective = activated  
viewing angle = 30  
position = 0 5849.72 0  
oversampling = 1  
up = 0 0 1  
lookat = 0 0 0  
resultsize = 256 256  
[perspective]  
status = activated  
[light1]  
diffuse = 0.333 0.333 0.333  
status = activated  
ambient = 0.333 0.333 0.333  
[light2]  
diffuse = 0.333 0.333 0.333  
status = not activated  
ambient = 0.333 0.333 0.333  
[angle]  
position = 0 0 0  
status = not activated  
right = 1 2 0  
left = -1 2 0  
[resolution]  
resolution = 0.1271  
unit = mm  
displayunit = mm  
[rendering]  
background = 0 0 0 255  
intensity = 0.333  
colormode = activated  
quickmode = activated  
algorithm = scatterhq  
{camera1}  
[viewer]  
perspective = activated  
viewingangle = 30  
position = 0 5849.72 0  
oversampling = 1  
up = 0 0 1  
lookat = 0 0 0  
resultsize = 256 256  
[perspective]  
status = activated  
[rendering]  
colormode = activated  
quickmode = activated  
algorithm = scatterhq

For the .raw file I have a txt file that comes with it… and it says only:  
Stitched\_RI\_H-neanderthal\_Gibraltar-1\_EM3811\_raw\_  
1558x1722x2870  
16 bits unsigned  
(uncheck Little-endian byte order)

Again I tried importing this with Raw Image Guess, but no luck!

Any help would be greatly appreciated!  
Thanks in advance

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [May 23, 2024, 2:52pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/2 "2024-05-23T14:52:46Z")

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Please give GEVolImport module in SlicerMorph extension a try. That should be able to import your dataset.

> **[SlicerMorph/GEVolImport at master · SlicerMorph/SlicerMorph](https://github.com/SlicerMorph/SlicerMorph/tree/master/GEVolImport#readme)**
>
> Extension to import microCT data and conduct 3D morphometrics in Slicer - SlicerMorph/SlicerMorph

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<div class="post-metadata">

**Author:** ![CatherineBone](https://avatars.discourse-cdn.com/v4/letter/c/f19dbf/32.png) [@CatherineBone](https://discourse.slicer.org/u/CatherineBone)\
**Post date:** [May 23, 2024, 3:01pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/3 "2024-05-23T15:01:57Z")

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Thank you @muratmaga. I dont have a pcr file though - only a .vol and .vgi  
Is there a way a .vgi can be turned into a .pcr?  
Thank you

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [May 23, 2024, 3:13pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/4 "2024-05-23T15:13:37Z")

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I don’t think so, but you can ask the imaging lab to give you that file. I think it is a standard output from GE scanners.

Or you can try and fiddle with RawImageGuess with those parameters.  
X Y Z should be 1374, 1401 and 2000  
and data type should be unsigned integer (unsigned 16 bit).

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<div class="post-metadata">

**Author:** ![CatherineBone](https://avatars.discourse-cdn.com/v4/letter/c/f19dbf/32.png) [@CatherineBone](https://discourse.slicer.org/u/CatherineBone)\
**Post date:** [May 23, 2024, 3:31pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/5 "2024-05-23T15:31:38Z")

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Thanks @muratmaga. Unfortunately those were the only files available from the Natural History Museum London. They wont be scanning the skull again any time soon.  
I tried RawImageGuess, but the XYZ can’t go beyond 1200 - so I can’t enter in 1374, 1401 and 2000.  
Is there another program that can access .vol files and turn them into dcm?

Also any suggestions on the .raw files? Again I tried RawImageGuess but the XYZ dimensions are too big for for module.

Thanks for your help

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [May 23, 2024, 4:10pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/6 "2024-05-23T16:10:39Z")

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> [@CatherineBone](#):
>
> RawImageGuess, but the XYZ can’t go beyond 1200 - so I can’t enter in 1374, 1401 and 2000.

@lassoan can you fix that limitation? Perhaps, provide a freehand entry for the size as opposed to a slider with upper bound?

@CatherineBone .pcr file is generated during the scan. So unless they deleted their data they should have it.

As an alternative, keep the XYZ dimensions as large as you can, set the spacing 0.1271 for all three, and then click **Generate NRRD Image Header** button. This will save a text file (NHRD), which you can open and then edit the XYZ dimensions correctly. You can then save it, and simply drag this file into slicer. Make sure that saved file (NHRD) sits in the same folder as the VOL file. If the settings are correct, then it should load fine.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [May 23, 2024, 4:21pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/7 "2024-05-23T16:21:20Z")

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> [@muratmaga](#):
>
> Perhaps, provide a freehand entry for the size as opposed to a slider with upper bound?

Using sliders is important to allow going through a range of values quickly. You can edit the range in the Advanced section:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/a/9a06bb3c93af3656a762e323f8ac92dc398eb6ee.png)

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [May 23, 2024, 10:25pm UTC](https://discourse.slicer.org/t/how-can-i-create-dcm-or-mesh-files-from-vol-and-vgi-files-and-raw/36346/8 "2024-05-23T22:25:17Z")

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> [@lassoan](#):
>
> Advanced section:

Good to know. I didn’t notice the Advanced section.