[Neuroimaging] NILEARN - WHY THIS CODE THROWS AN ERROR?????
Christopher Markiewicz
markiewicz at stanford.edu
Fri Jul 8 09:40:35 EDT 2022
A lack of traceback makes it difficult to see where the error is occurring, but I believe the issue is that you're passing a numpy array to a nilearn function that expects an image.
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________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of נתי שטרן <nsh531 at gmail.com>
Sent: Friday, July 8, 2022 9:38:57 AM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: Re: [Neuroimaging] NILEARN - WHY THIS CODE THROWS AN ERROR?????
it's a fullpath to nifti image
בתאריך יום ו׳, 8 ביולי 2022 ב-16:27 מאת Matthew Brett <matthew.brett at gmail.com<mailto:matthew.brett at gmail.com>>:
Hi,
On Fri, Jul 8, 2022 at 2:05 PM נתי שטרן <nsh531 at gmail.com<mailto:nsh531 at gmail.com>> wrote:
>
> fullcode:
>
>
>
> import nilearn.plotting as plot
> import os,gzip,io
> import nibabel as nib
> path="C:/users/administrator/desktop/nii"
> path2="C:/users/administrator/desktop/nii/out/"
> for i in os.listdir(path):
> if(".nii.gz" in i):
> pass
> else:
>
> if(".nii" in i):
> img = nib.load(path+"/"+i)
> data = img.get_fdata()
> print(data)
> import imageio
> X=0
> for s in data:
> import numpy
> aleph=numpy.array(s,dtype=numpy.int8)
> X=X+1
> plot.plot_img(aleph)
>
> imageio.imwrite("C:\\users\\administrator\\desktop\\nii\\"+i+str(X)+'.jpg', s)
>
>
>
>
>
>
> error:
> Data given cannot be loaded because it is not compatible with nibabel format
Honestly - I wouldn't email python-list - this is a neuroimaging question.
The obvious debugging step here is to see what "path+"/"+i" is. Is it
in fact a filename of a nifti image? Try loading it in some other
Nifti reader. If you get stuck, put the file up somewhere where we
can get it and try loading it.
Cheers,
Matthew
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