I do not know how to use this package in both Windows command line environment and Python 3 Jupyter Notebook environment. If you could explain how to use med2image? The description on https://pypi.org/project/med2image/#description is insufficient to explain how to use this package. Thanks.

[sivaskandha]

I do not know how to use this package in both Windows command line environment and Python 3 Jupyter Notebook environment. If you could explain how to use med2image? The description on https://pypi.org/project/med2image/#description is insufficient to explain how to use this package. Thanks.

Originally posted by @mangozy in #8 (comment)

[xihuanliuliu]

can u slove the problem?

[javierrodenas]

Same problem!

[rudolphpienaar]

Have you looked at the updated README? We also now provide a docker version in the pl-med2img repo.

But looking at your very initial report, I guess my first naive question to you is, "are you in the correct dir?" The Windows error message seems quite clear: "not recognized as an internal or external command..." suggests to me that the script is not on your path.

Alternatively, you might want to prefix the command with "python3..." , ie

python3 med2image ...

Having said all this, unfortunately we don't typically have or develop to Windows so it's hard to debug.

[rudolphpienaar]

Also, from an python import you don't run the command as though it were a command line. Your jupyter notebook command makes no sense. If you import the module you should call it from its python API. Does this make sense?

[miguel961804]

Someone found how to run on windows, the script is supposed to run but it does not generate any image, I would appreciate the support

[rudolphpienaar]

@miguel961804 -- can you provide a better help/issue request? Saying it didn't work, other than conveying that something went wrong, doesn't help us. At the very least, please provide the exact CLI you used and also what led you to conclude that it didn't work. Or did you do this in a jupyter notebook? Whatever it is that you did, you have to give us enough info to replicate.

Does that make sense?

[dimasquest]

works in jupyter if you add ! before running the command
working example below:
! med2image -i hippocampus_img.nii -d out_hippl

[shun2311]

python E:\Anaconda\Lib\site-packages\med2image\med2image.py -i SMIR.Brain.XX.O.CT.339336.nii -d out
I tried running with the command above and it did not show any error, however no image is generated

[sparklerl]

run med2image on windows like this

need change the "nimg.get_data()" to "nimg.get_fdata()" ,the nibabel new version change the function name?

good luck!