Operating system:windows 7 Slicer version:both slicer 4.6 and 4.7 I made a segmentation and clip a volume with module,then how can i get the intensity value of each voxel list in a spreadsheet?the coordinate is not necessary.thanks

Probably Segment statistics module provides this information. If not, then please describe in more detail what exactly you would need.

I need the data of every voxel which have been shown at data probe,just simply a list of voxel value,coordinate included is fine,but not the statistical parametre of them. maybe it would be like: x,y,z,value … … …

Probably the simplest would be to get the volume as a numpy array and then write out the voxel indices and values you are interested in. Something like this (this outputs all voxels that has value >260): import numpy as np voxelArray = slicer.util.arrayFromVolume(getNode('MRHead')) indices = np.whe…

it’s awesome,thank you very much,it’a great help:smiley::smiley:

[image] lassoan: If you need physical (RAS) coordinates instead of voxel coordinates (IJK) then you have to multiply the (x,y,z,1) vector from the left with the volume’s IJKToRAS matrix. I still try to convert ijk to LPS? Is it possible to provide an example for the vector multiplication? Tha…

Search for “ijktoras.multiplypoint” in Slicer script repository for examples.

Hi Andras, I used the arrayfromvolume to get the voxel intensities for an mri. but when i use the same mri to get the voxel intensities outside slicer using python and reading nrrd file I get different intensities. Do you have any idea why its happening? thank you Regards, Saima safdar

NRRD file format is very simple, so it is unlikely that different values are decoded from the file. Probably you just read the value from a different location. There are two conventions for voxel indexing (IJK vs. KJI), so try reversing order of voxel coordinates. Also note that internally Slicer us…

Dear all, how should I write the same script in order to print the result in an external txt file? thank you very much

Since you get the voxels in a numpy array, you can use standard Python and numpy functions to write it to file. An example is provided above . Note that apart from the slicer.util.arrayFromVolume function to get the numpy array, everything else is plain Python and numpy.

How to export voxel intensity

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How to export voxel intensity

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