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Can't get the full volume using actual thickness. #20

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ArnoBlue opened this issue Jun 26, 2024 · 1 comment
Open

Can't get the full volume using actual thickness. #20

ArnoBlue opened this issue Jun 26, 2024 · 1 comment

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@ArnoBlue
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ArnoBlue commented Jun 26, 2024

Hi NeSVoR team,

Thank you so much for making the code public! I tried to reproduce your results using the CRL atlas dataset. But found that I need to enter a larger parameter than the actual thickness to get the full volume.

I used the following code to get to the thickness of the data as [0.8,0.8,0.8].
img = nib.load(nii_file)
#turn into numpy
data = img.get_fdata()
affine = img.affine
resolution = affine.diagonal()[:3]

I used the following command for SVR:

nesvor reconstruct
--input-stacks .../STA33.nii.gz .../STA33.nii.gz .../STA33.nii.gz
--thicknesses 0.8 0.8 0.8
--output-volume .../3316.nii.gz
--bias-field-correction
--output-resolution 0.8

However, I got an incomplete volume:

image

If I change the command to
--thicknesses 1.4 1.4 1.4
I can then get the full volume:

image

@ArnoBlue
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I have noticed that the results I get are similar to those in 'Cannot reproduce results on FeTA using your slicing strategy' (a closed issue). Could you clarify what are the limitations of the thickness parameter?

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