# Loading files from a GE microCT 

**URL:** <https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937>\
**Category:** Support\
**Created:** [January 26, 2018, 1:06am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937 "2018-01-26T01:06:23Z")\
**Posts on this page:** 13\
**Page:** 2

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**Author:** ![Jeff\_Zeyl](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jeff_zeyl/32/70056_2.png) [@Jeff\_Zeyl](https://discourse.slicer.org/u/Jeff_Zeyl)\
**Post date:** [September 28, 2020, 5:50am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/21 "2020-09-28T05:50:01Z")

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Sorry for the confusion - I mixed my reference to two different volumes I was testing. Yes, that one (1737x1139x2022) is about 7.8 GB. Another smaller one (1119x1338x1294) is 3.6 GB. Both had the same issue. Here’s the example vgi info associated with the vol file:

{volume1}  
[representation]  
size = 1737 1139 2022  
bitsperelement = 16  
datatype = unsigned integer  
datarange = 0 65535  
[file1]  
Mirror = 0 1 1  
RegionOfInterestStart = 0 0 0  
RegionOfInterestEnd = 1736 1138 2021  
FileFormat = raw  
Size = 1737 1139 2022  
Name = X:\24082020 Jeff\24082020\_02 WBC-01-2020\24082020\_02 WBC-01-2020.vol  
bitsperelement = 16  
datatype = unsigned integer  
datarange = 0 65535  
[description]  
text = 0  
{default}  
[version]  
release = VGStudioMax 1.0  
{volumeprimitive9}  
[section1]  
max = 65535  
offset = 0  
min = 0  
name = section [0]  
[geometry]  
clipplane1 = -1 0 0 1737  
clipbox = 0 0 0 1737 1139 2022  
position = 0 0 0  
status = visible  
relativeposition = 0 0 0  
resolution = 0.050000 0.050000 0.050000  
center = 868 569 1011  
scale = 1 1 1  
rotate = 1 0 0 0 1 0 0 0 1  
unit = mm  
[volume]  
volume = volume1  
[description]  
text = X:\24082020 Jeff\24082020\_02 WBC-01-2020\24082020\_02 WBC-01-2020.vol  
[segment1]  
opacityvalue = 0.0 2.0  
status = activated  
description = 0  
redvalue = 255 255  
greenvalue = 255 255  
bluevalue = 255 255  
redx = 0 65535  
greenx = 0 65535  
bluex = 0 65535  
opacityx = 0 65535

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**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:** [September 28, 2020, 3:22pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/22 "2020-09-28T15:22:50Z")

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Can you share an example image (upload to dropbox/onedrive/google drive/… and post the link here) so that we can investigate?

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/83011_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [September 28, 2020, 8:59pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/23 "2020-09-28T20:59:19Z")

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VGStudio Max log file indicates data is 16 bit unsigned. Is that what you set in the Raw Image Guess too?  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/a/aad50a3d372fa02bb41f56ad7f60f796d7e9e277.png)

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<div class="post-metadata">

**Author:** ![Jeff\_Zeyl](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jeff_zeyl/32/70056_2.png) [@Jeff\_Zeyl](https://discourse.slicer.org/u/Jeff_Zeyl)\
**Post date:** [September 30, 2020, 10:17am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/24 "2020-09-30T10:17:16Z")

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Yes, I selected 16 bit unsigned and little endian. Here’s the input and what it loads:

> **[rawimageguess - Google Drive](https://drive.google.com/drive/folders/1CqWU2-0Txe8Fq-FjigHf6nW2Da8R9rLP?usp=sharing)**

  
The first two pics show it loaded fine (a bird neck shown in the volume), but then at 27.1 mm it clips part of the image, and all subsequent images are black. I also noticed the contrast for the loaded volume can’t be adjusted in the usual way using the mouse; not sure if that’s related to this problem

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/83011_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [September 30, 2020, 2:51pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/25 "2020-09-30T14:51:23Z")

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Is it possible for you to upload the vol file on the google drive?

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<div class="post-metadata">

**Author:** ![Jeff\_Zeyl](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jeff_zeyl/32/70056_2.png) [@Jeff\_Zeyl](https://discourse.slicer.org/u/Jeff_Zeyl)\
**Post date:** [October 1, 2020, 7:25am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/26 "2020-10-01T07:25:24Z")

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I’ve added an example vol and vgi in the folder

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/83011_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [October 1, 2020, 5:08pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/27 "2020-10-01T17:08:37Z")

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Thanks.  
@lassoan I am getting this error on windows 4.11.0-2020-09-21 r29383 / c299952

```
Warning: In D:\D\P\Slicer-0-build\VTK\IO\Image\vtkImageReader2.cxx, line 687
vtkImageReader2 (000001CD8B5971B0): File operation failed.
Generic Warning: In D:\D\P\Slicer-0-build\VTK\IO\Image\vtkImageReader2.cxx, line 757
File operation failed. row = 630, Read = 3026, FilePos = -1

```

And also the load dialog box for file browser opens as save as.

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/83011_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [August 15, 2022, 3:59am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/28 "2022-08-15T03:59:24Z")

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To close the loop on this:

There is now a simple utility module (VoIImportModule) which allows to obtain the image spacing and dimensions provided by the PCR file. The instructions to install the module and how to use it can be found at:

> **[GitHub - chz31/VolImportModule](https://github.com/chz31/VolImportModule/)**
>
> Contribute to chz31/VolImportModule development by creating an account on GitHub.

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**Author:** ![jusopar](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jusopar/32/10144_2.png) [@jusopar](https://discourse.slicer.org/u/jusopar)\
**Post date:** [February 21, 2023, 1:45am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/29 "2023-02-21T01:45:01Z")

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Hi Murat,  
Thank you for this helpful module!  
But I’m not able to find it in 3Dslicer after following the installation steps. I cloned the repository, added the additional module path and restarted 3D slicer. But when I open it again, I cannot find the module. I searched as VolImport or GEVolImport, and nothing is showing up.  
Did I miss a step to get the module installed?  
Thanks!  
Julia

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/83011_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 21, 2023, 6:14am UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/30 "2023-02-21T06:14:19Z")

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@jusopar This is now incorporated to the SlicerMorph module as a development tool (since more testing needs to be done).

Just update your SlicerMorph to the latest version (from extension manager). Then go to **Edit-\>Application Settings-\>Developer** and enable “ **Developer Mode** ”. After this you can use the Module Search (CTRL+F) and search for “GEVol”. You also need to enable the “testing” option (see screenshot).

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/0/6001410d864507070d32ac90b5c2ec1875e232de.png)

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<div class="post-metadata">

**Author:** ![jusopar](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jusopar/32/10144_2.png) [@jusopar](https://discourse.slicer.org/u/jusopar)\
**Post date:** [February 21, 2023, 5:00pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/31 "2023-02-21T17:00:26Z")

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It worked! Thank you so much!

If I don’t use this development tool, what information form the .pcr file I should use to figure out the image spacing, when importing via Image Stack?

On another topic, how can I enable the scale bar (ruler) for the purpose of capturing a screenshot to be used in a figure in a publication?

Thanks so much again!

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/83011_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 21, 2023, 5:19pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/32 "2023-02-21T17:19:24Z")

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The only piece of informaiton you

> [@jusopar](#):
>
> If I don’t use this development tool, what information form the .pcr file I should use to figure out the image spacing, when importing via Image Stack?

Image spacing. You need to dig that out from the pcr file. I think everything else should be fine.

> [@jusopar](#):
>
> On another topic, how can I enable the scale bar (ruler) for the purpose of capturing a screenshot to be used in a figure in a publication?

if you used this tool (or Imagestacks and provided the right image spacing), your data is already correctly scaled, and you can enable the rulers both in 2D and 3D. In 3D, you need to use the orthographic projection for the ruler to be visible (most people by default use the perspective rendering).

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/d/2d61ff8a1069c4facbbf4015dbfbfc2afb52896c.jpeg)

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<div class="post-metadata">

**Author:** ![jusopar](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jusopar/32/10144_2.png) [@jusopar](https://discourse.slicer.org/u/jusopar)\
**Post date:** [February 21, 2023, 5:32pm UTC](https://discourse.slicer.org/t/loading-files-from-a-ge-microct/1937/33 "2023-02-21T17:32:49Z")

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Perfect! Thank you so much!

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