I have not used FIJI/ ImageJ for CT data visualization, but I think you can use Slicer/ Mimics for this, and such rescaling never happens in these tools. Else, you can rescale the changed volume back to original.

Hi Frantisek,

interesting. i use fiji for 3D x-ray CT data (raw volumes and tiff stacks) regularly but have not come across this particular problem.

Please can you tell how you are importing and then saving your dataset?

thanks,

sharif

The story so far:

I have done my reconstructions in NRecon with BMP-files as an output. Then I wanted to remove some artifacts, so I loaded the data to FiJi (Import > Image Sequence with increment 1 and scaling 100%). Then I saved the files as BMP again (Save As > Image Sequence). No transformations.

After loading the modified data to CTVox together with the original reconstruction, I have realized, they do not match.  Moreover, the ratio of voxel-size change is quite bizarre: from 35um to some 128um.

This makes me suspicious, there is some automatic voxel-size in FiJi (or BMP processing) and I just do not know, where to say him to do otherwise.

For reconstruction it is OK, but I need to measure some volumes too.

And yes, I know about Mimics, Avizo etc., but we do not have them yet, so I must find a solution for FiJi.

ok.

when you have imported the original dataset, you should see something like:-

'2000x2000pixels; 16bit;7.6MB'

if on the other hand you see something like:

 '200x200 mm (2000x2000); 16bit; 7.6MB'

this could explain why you are getting different voxel size after importing a fiji saved dataset. simply clear any preset voxel/pixel scaling  -> Analyze -> Set Scale -> Click to remove scale. tick 'global.

Also try saving as a 'tif' instead of bmp.

Thanks, I will try it ASAP.