madsendennis/notebooks

Python notebooks

Python notebooks

Code material for the youtube channel: https://www.youtube.com/channel/UC8fwFSM3zKpa-huYkubwEpA

notebooks's Issues

Unable to get 3D volume in part 3 Even after running all the code without error.

Hello Sir,
We are following your video which is available on your You tube account for teeth segmentation (https://youtu.be/NSyEbJ7Phis).
We are using that code for liver segmentation. But while we were running the code, we came across some errors in part 3 video.
Which are listed as follows:

1. we are unable to use marching_cubes_lewiner instead of that we used marching_cubes.
2. we did not get any 3D-volume after this command {mp.plot(vertices, faces, return_plot=False)} as you got in you tube video.
   Link for my Goggle Colab. I request you to visit the link for better understanding of our problem :- usp=sharinghttps://colab.research.google.com/drive/1crKpq4kSRDxl2cwyAnyorWl00jcSgIhn?usp=sharing
   Also would it be possible for you to share the data set for teeth segmentation so we can get some idea how the code works and resolve our errors.

It would be of great help if you can help to solve the above mentioned error.

Not showing results from print image and mask volumes

Hi!
Before that, i have following all the code that you made and i didn't have the error so far but i have trouble that in the print function from this,

for index, filename in enumerate(sorted(glob.iglob(imagePathInput+'*.nii'))):
img = readImageVolume(filename, True)
print(filename, img.shape, np.sum(img.shape), np.min(img), np.max(img))
numOfSlices = sliceAndSaveVolumeImage(img, 'aorta1'+str(index), maskSliceOutput)
print(f'\n{filename}, {numOfSlices} slices created \n')

also in

for index, filename in enumerate(sorted(glob.iglob(maskPathInput+'*.nii'))):
img = readImageVolume(filename, True)
print(filename, img.shape, np.sum(img.shape), np.min(img), np.max(img))
numOfSlices = sliceAndSaveVolumeImage(img, 'aorta1'+str(index), maskSliceOutput)
print(f'\n{filename}, {numOfSlices} slices created \n')

didn't showing the results and didn't have an error, only the result is not showing. And also at the end, my number files that must contain all the slices is only showing 1, not all the slices that i have from the input data which is it must be 186 slices

Hoping u would answer and help me, thank you!

Part 1 - Pre-processing - Number of masks less than number of slices

Hi ! Thanks for theses great notebooks.

I'm working on MRI and segmented it using 3DSlicer. I converted the .nrrd files into .nii.
When I run the Part 1 notebook to save my volumes in slices, the number of slices containing my masks is lower then my total number of mri slices (I'm missing around 900 masks images). I have been searching why but I still have no explanation.
Would you have an idea ?

Save

Hi! How can we save predicted mask to a nifti format?