ROI Intensity using Python

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1

Hi,

I want to calculate average pet intensity within given ROI. I have two images: (1) PET registered on CT and (2) ROI registered on CT. I can do this in MATLAB but I want to try with python. Does anyone have python solution similar to this? I am new to python.

Here is the MATLAB code:

pet_image = niftiread(‘pet_on_ct.nii.gz’);
roi_image = niftiread(‘ROI_MNI_on_ct.nii.gz’);
index_all = unique(roi_image(:));
result=[];
for i = 1:length(index_all)
index = index_all(i)
pet_intensity_within_given_roi=pet_image(find(roi_image==index));
result=[result; mean(pet_intensity_within_given_roi)];
end;

Thanks.

2

have you solved it？ i also want to know and use it

3

I use nipype with fslstats Neuroimaging in Python - Pipelines and Interfaces — nipy pipeline and interfaces package ImageStats with -K -M. Not pure python, but easy to use.

4

could you provide the python code for roi extraction of pet

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from nipype.interfaces.fsl import ImageStats
stats = ImageStats()
stats.inputs.in_file = 'pet.nii.gz'
stats.inputs.op_string = '-M'
stats.intputs.index_mask_file = 'mask.nii.gz'
result = stats.run()
6

Thx very much，， i will try later… if any questions i will leave a message… thx