Loading files from a GE microCT

Support
21

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

22

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

23

VGStudio Max log file indicates data is 16 bit unsigned. Is that what you set in the Raw Image Guess too?
image

24

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


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
25

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

26

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

27

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.

28

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:

1 Like
29

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

30

@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
image848×515 33.5 KB

31

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!

32

The only piece of informaiton you

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

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
image875×1202 91.5 KB

1 Like
33

Perfect! Thank you so much!