Dear RG Community,

I've been following the steps proposed Buser et al (2020) and I'm running into some difficulties.

I load the image stack into Fiji and follow all the steps until I save the file in a .nrrd format to load in 3D Slicer.

When I open the .nrrd file in 3D Slider, the file has a lot of issues (image below with arrows pointing to issues).

I think, I might be making some mistake when specifying voxel size in Fiji.

Does anyone knows how to fix this ? Or where I might be wrong ?

Thanks

Information on the scan:

[Reconstruction Settings]

FreeRay=8198

UseFreeRayFromPCP=1

CorrectionValue=11.23999977111816

ObjectRotation=62.25

RecFilterKernel=2

ROI_Filter=1

StartImage=1

LastImage=1440

ImageFilter=1

VolumeFilter=1

VolumeGaussRadius=3

VolumeUSMContrast=50

VolumeUSMIterations=2

VolumeUSMRadius=3

[VolumeData]

Volume_SizeX=1116

Volume_SizeY=1190

Volume_SizeZ=2013

VoxelSizeRec=0.01173949521034956

Resolution=1

Format=5

Min=-0.02392741106450558

Max=0.2697736620903015

Reference:

T J Buser, O F Boyd, Á Cortés, C M Donatelli, M A Kolmann, J L Luparell, J A Pfeiffenberger, B L Sidlauskas, A P Summers, The Natural Historian's Guide to the CT Galaxy: Step-by-Step Instructions for Preparing and Analyzing Computed Tomographic (CT) Data Using Cross-Platform, Open Access Software, Integrative Organismal Biology, Volume 2, Issue 1, 2020, obaa009,