How ITK Snap gets the intensity at a particular co-ordinate from the MRI Scan, and which library does the ITK Snap to get intensity at a particular co-ordinate

[NiharJani2002]

I am doing Brain Tumour Segmentation. I am analysing BRATS 2020 dataset. If I hover over a particular co-ordinate (let the co-ordinate be [x,y,z]) in MRI scan using ITK snap, I get a particular intensity value.

My Question is How to get that particular intensity in the Python code or c++ code ? Such that I can it.

If possible share the code also, or what algorithm does ITK Snap uses to show that particular intensity from MRI Scan

[NiharJani2002]

I am using PyTorch, but I can move on to Tensorflow if its works well with Tensorflow

[liamtimms]

In case this wasn't clear, you can use ITK itself (python and c++) or simpleITK to get that behavior. ITK snap is a GUI built on ITK.

[NiharJani2002]

Thanks @liamtimms , but I am using the ITK library in my code but still I am not getting the same intensity values when matched to ITK snap software. Can you pls guide me how to Get it?

[liamtimms]

@NiharJani2002 I am not associated with ITK or ITKsnap, but you can find information about accessing pixel values and interpolation in the ITK book: https://itk.org/ItkSoftwareGuide.pdf or use the simpler nibabel -> numpy in python by just indexing to the voxel of interest if you are less interested in spatial coordinate.

[pyushkevich]

Pixel values are very easy to access with SimpleITK. You just have to watch out for coordinate swaps, so for example x,y,z in Numpy maps to z,y,x in SimpleITK/ITK-SNAP. In ITK-SNAP the image coordinates (row,column,slice) displayed to the user have 1-based indexing, i.e., if you have 5 slices, they are numbered 1,2,3,4,5, rather than 0,1,2,3,4 as in Python/NumPy arrays. So that might be the source of the mismatch. In the early 2000s, when SNAP was first developed, most people outside of C/C++ were not used to 0-based indexing, so we thought 1-based would be more intuitive for our target audience. Changing it now would make things confusing for users. Finally, prior to version 4.2, ITK-SNAP internally represented all images as int16. So when an image with floating point intensity values was loaded, those values were mapped to the range between 0 and 2^16-1, resulting in some loss of precision. Since 4.2, floating point intensity values are stored as such. Best, Paul

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On Thu, Jul 18, 2024 at 11:41 PM Liam Timms, PhD ***@***.***> wrote: @NiharJani2002 <https://github.com/NiharJani2002> I am not associated with ITK or ITKsnap, but you can find information about accessing pixel values and interpolation in the ITK book: https://itk.org/ItkSoftwareGuide.pdf or use the simpler nibabel -> numpy in python by just indexing to the voxel of interest if you are less interested in spatial coordinate. — Reply to this email directly, view it on GitHub <#117 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJPEW7P5J5P5URHNBFHWMLZNAZBZAVCNFSM6AAAAABKKMZW6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZXGY3TANZXHE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>