alexlaurence / nifti-image-converter Goto Github PK

Hello 🙂!
Great program ! I understood how to use it from the terminal only I have a large number of convert exams and I would have liked to know how I could iterate on it? It does not seem to me that this is possible via the terminal?

Hello ,
First of all thank you so much for this incredible work

OK, so The nii2png. worked with me so well to convert nifti file to PNG images by using Matlab. my question is how to use it to convert more than one thousand nifti images that I need to convert to PNG?

I am working in Google colaboratory
I installed using pip install nii2png command, i was able to do it successfully.
then i ran $ python3 nii2png.py -i /content/MICCAI_BraTS_2019_Data_Training/HGG/BraTS19_2013_10_1/BraTS19_2013_10_1_flair.nii -o /content/output_nifti_png/
and it gave an error as
/bin/bash: nii2png.py: command not found
what should i do?

Hi there!

I noticed in your nii2png matlab program there was an error on line 173. You forgot to change the increment name from i to current_slice causing it to stay in an infinite loop! Simple fix.

I am using python 3.7 using the following packages in python virtual environment

Package Version

nibabel 2.4.1
numpy 1.16.4
pip 19.1.1
scipy 1.3.0
setuptools 40.8.0
six 1.12.0

But, I get the bellow error :

$ python nii2png.py -i /home/mike/Downloads/dgan/0001.nii -o test.png
Traceback (most recent call last):
  File "nii2png.py", line 14, in <module>
    import scipy, numpy, shutil, os, nibabel
  File "/home/mike/Downloads/dgan/venv37/lib/python3.7/site-packages/nibabel/__init__.py", line 51, in <module>
    from . import analyze as ana
  File "/home/mike/Downloads/dgan/venv37/lib/python3.7/site-packages/nibabel/analyze.py", line 87, in <module>
    from .volumeutils import (native_code, swapped_code, make_dt_codes,
  File "/home/mike/Downloads/dgan/venv37/lib/python3.7/site-packages/nibabel/volumeutils.py", line 23, in <module>
    from .openers import Opener, BZ2File
  File "/home/mike/Downloads/dgan/venv37/lib/python3.7/site-packages/nibabel/openers.py", line 16, in <module>
    from bz2 import BZ2File
  File "/usr/local/lib/python3.7/bz2.py", line 19, in <module>
    from _bz2 import BZ2Compressor, BZ2Decompressor
ModuleNotFoundError: No module named '_bz2'

I need help with preprocessing medical image data.

I have 100 nifti images.

I want to extract 5 slices from each of these as jpegs.

However, I work in a particular contrast setting with my nifti files when I segment them. How do I ensure that the jpeg file is in my contrast window?

For eg, I open my nifti in ITK snap and change the window to 60-360 and look at the visibility in that setting. This is lost on conversion though.

Is there any way to do this via your software or otherwise? Thanks

Why i got this error?

Traceback (most recent call last):
File "nii2png.py", line 157, in
main(sys.argv[1:])
File "nii2png.py", line 38, in main
image_array = nibabel.load(inputfile).get_data()
File "C:\Users\rit\Anaconda3\lib\site-packages\nibabel\loadsave.py", line 56, in load
filename)
nibabel.filebasedimages.ImageFileError: Cannot work out file type of

Hello,
I was trying to use that script for an output image of ANTS.
My nifti file is 2D (only has 1 slice). Maybe one can add this functionallty
Thank you

The output image dimension for coronal and sagittal (x and y axis) were all squeezed to incorrect shape. In my case, the 512x512 image becomes 512x120. Is there any way to ensure the output scale or dimension? Really appreciate if anyone could help. I have been finding a solution for days with no luck. Thank you.

Hello sir I am using repo and here I am getting stuck what is means and what is the proper solution of this error and furthermore please give me suggestion that whether I would solve this error using different data file?
I am using ADNI dataset and my extension is in .nii.
Thanks in advance
Error:
User selected C:\Users\Ali ktk\Desktop\AD Codes\NIfTI-Image-Converter-0.2.9.9\NIfTI-Image-Converter-0.2.9.9\nii\002_S_0413.nii
Error using affine3d/set.T (line 340)
The final column of an affine transformation matrix must consist of zeroes, except for a one in the last row.

Error in affine3d (line 117)
self.T = A;

Error in images.internal.nifti.niftiImage/getXForm (line 506)
xform = affine3d([R zeros(3,1); T 1]');

Error in images.internal.nifti.niftiImage/simplifyStruct (line 162)
[XformName, Xform] = self.getXForm();

Error in niftiinfo (line 50)
simpleStruct = NV.simplifyStruct();

Error in nii2png (line 27)
image_info = niftiinfo(fullfile(path,file));

I have the dataset with four classes . I want to convert the NIFTI images to jpg to develop a model for classification

I am still debugging this segments of the code:
base_path=os.path.abspath(os.path.dirname(file))
parser = argparse.ArgumentParser(description='Arguments for input and output files')
parser.add_argument('--input_path', type=str, default = base_path, help='Path of the input files')
parser.add_argument('--rotation_angle', type=int, default = 90, help='Rotation degree, i.e., 90°, 180°, 270°, default value is 90°')
args = parser.parse_args()
input_path = args.input_path
rotation_angle = args.rotation_angle
##############################################################
#get list of nii or nii.gz source files
source_files = os.listdir(input_path)
slice_counter = 0
#identify sample ids and get source ids
source_ids = [files[0:8] for files in source_files if files.endswith('.nii')]

sample_ids = list(set(source_ids))

hi am using the matlab code and i want to get images with 3 channels (RGB images) instead of grayscale images,
how should i change the code to do this

help pleaaase!

Hi,
First of all thanks for writing such awesome code for helping others.

Now let's come to my problem. I was trying to use your code for my research. I successfully used "nii2png.py" to convert a single 3D nifti file. But did not find the use of "nii_to_png_converter.py" anywhere in your documentation. Can you please explain how to use it? That would be of great help. Thank you.

Sincerely,
Shabbir

I am trying to install it using admin and facing following problem !

Collecting shutil (from nii2png)
Could not find a version that satisfies the requirement shutil (from nii2png) (from versions: )
No matching distribution found for shutil (from nii2png)

can we convert .nii to .jpg slices using nii2png

According to the scipy documentation, the scipy.misc.imsave function is deprecated. More so, it has been completely removed in newer scipy 1.3+ versions, so that nii2png now fails:

$ python nii2png.py -i in.png -o foo/
Reading NIfTI file...
Saving image...
Traceback (most recent call last):
  File "nii2png.py", line 158, in <module>
    main(sys.argv[1:])
  File "nii2png.py", line 142, in main
    scipy.misc.imsave(image_name, data)
AttributeError: module 'scipy.misc' has no attribute 'imsave'

However, the documentation linked above does recommend another way to save images.

Hi!
While trying to run from the code in latest stable zip file, I am getting this error:

Traceback (most recent call last):
  File "nii2png.py", line 159, in <module>
    main(sys.argv[1:])
  File "nii2png.py", line 42, in main
    data_4d = image_array[:, :, i, j]
UnboundLocalError: local variable 'i' referenced before assignment

What are these i and j variables for?

thank you for the code
When I convert the images, I get a black image.png.
I have no idea why i am getting a black picture.
Can anyone help me?
@monjoybme & @alexlaurence
Many Thanks