CT scan files and Large Image Stacks

[David Thomas]

Hi Everybody -

I have CT scan data that I would like to work with. 

The scan data is all in a folder called "NSI exe". There are 7 files that have sequential numerical extensions (.001, .002,... .007). They are large (~2GB) files that appear to be binary. I can not read them, but there is a .exe file in the folder that opens an app called efXCT that displays the part. It can also export image slices and STL volumes. 

I have a couple of obstacles confounding me today:

1. Does anybody know how to import these files?  efXCT is made by NSI (North Star Imaging), so it's likely a proprietary thing, but wondering if anybody's cracked that nut?
   
2. The image stacks generated are huge (1725 x 1450 x 1725), and trying to use Import Images (3D Stack) causes my computer to crash. Is there a way to import the images at a reduced resolution?
   

Thanks,

Dave

[Michael Jackson]

Hello,

    I think the best way to move forward would be to have the efx-CT software dump a stack of images. Then have something like FIJI or MATLAB or Python resize the images for you to something smaller. With the current size of the CT scan and assuming 8 bit images you would need 4,314,656,250 bytes (4.3 GiB) just to read the data into DREAM.3D. That is one large contiguous chunk of RAM available. If the images were RGB then you need 3x that amount. Once the images are resized then you can import them into DREAM.3D to perform your analysis.

That is a nice suggestion to resize the images during import to a lower resolution.

 

https://github.com/BlueQuartzSoftware/ITKImageProcessing/issues/155

https://github.com/BlueQuartzSoftware/ITKImageProcessing/issues/156

 

 

--
Mike Jackson

 

 

 

On 5/2/18, 4:43 PM, "David Thomas" <dream3...@googlegroups.com on behalf of davidrob...@gmail.com> wrote:

 

Hi Everybody -

 

I have CT scan data that I would like to work with. 

 

The scan data is all in a folder called "NSI exe". There are 7 files that have sequential numerical extensions (.001, .002,... .007). They are large (~2GB) files that appear to be binary. I can not read them, but there is a .exe file in the folder that opens an app called efXCT that displays the part. It can also export image slices and STL volumes. 

 

I have a couple of obstacles confounding me today:

1.       Does anybody know how to import these files?  efXCT is made by NSI (North Star Imaging), so it's likely a proprietary thing, but wondering if anybody's cracked that nut?

2.       The image stacks generated are huge (1725 x 1450 x 1725), and trying to use Import Images (3D Stack) causes my computer to crash. Is there a way to import the images at a reduced resolution?

Thanks,

Dave

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