How to create a histogram of a nifti file

[sishan]

Hi,
I'm trying to create a histogram of a .nii file but it's now working.
1. loading the nifti file:
>> Try2=load_nifti('DM.nii');
2. hist(Try2);
that generarates a histogram, where most of the values are concentrated between -150 and 200.(3 bars,the middle one is between -50 and 100).
3. I then use a function that sets all pixels in the range to 1 (white)
and all pixels that are out of range to 0 (black).
range=(inputFileName >= I_min & inputFileName <= i_max);
inputFileName(range)=1;
inputFileName(~range)=0;

4. Then I save the file and open it with ITKSnap
save_nifti(inputFileName,outputFileName,1);
but when I open it, it's almost all white.

Not sure what I'm doing wrong, please help.
Thanks in advance!

 

[KataKoniK]

Hi there,

It seems like the issue may be in the way you are setting the pixels to 1 or 0. When creating a histogram, it's important to consider the range of values in the image and how they are being represented. It's possible that the majority of your image has values between -150 and 200, so when you set all pixels within that range to 1, it may be causing the entire image to appear white.

One suggestion would be to adjust the range of values you are setting to 1 or 0. Instead of using -150 and 200, try using a smaller range that encompasses the majority of your image values. You could also try using a different function to set the pixels, such as a thresholding function, to better isolate the values you want to represent in the histogram.

Additionally, make sure you are saving the file correctly and that the values are being saved as integers rather than floats. This could also affect how the image appears when opened in ITKSnap.

I hope this helps and good luck with your histogram! Let me know if you have any further questions or if this solution works for you.