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.

Get Outlook for Android<https://aka.ms/AAb9ysg>
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>‬‏>:‬

‪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.


Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20220708/d1f71e28/attachment.html>

More information about the Neuroimaging mailing list