I am fresher to digital image processing.my data contains,annotated each lesion in each ct scan by drawing a 3D bounding box wrapping around the lession from the axial, coronal ,sagittal direction as close as possible.each lesion corresponds to an annotation consisting of the coordinates and length of the groundtruth box in three dimension.The CT scan are in .nii format,and the annotation are in .csv format.
One option is to load in ImageJ, and then use the orthogonal views to define your bounding boxes.
itksnap (http://www.itksnap.org/pmwiki/pmwiki.php) handles nifti-formats and is easy to use.
If you want to perform more operations on the data then you can use R and load the data by using the oro.nifti library (https://rdrr.io/cran/oro.nifti/man/).
There are also a lot of really useful tools you can explore in the (https://neuroconductor.org/list-packages/all) most are focused on neuro-imaging and MRI, but some are also useful for other organ systems and modalities.
If you want to explore images inside of R-studio then PapayaR (https://rdrr.io/cran/papayar/man/papaya.html) is a really practical solution where you can view 3-D images within R-studio.
Hope this helps, best of luck to you.
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