<div dir="rtl"><div dir="ltr">HOW TO DO THIS? </div><div dir="ltr">I'm new in numpy :) </div></div><br><div class="gmail_quote"><div dir="rtl" class="gmail_attr">‫בתאריך יום ו׳, 8 ביולי 2022 ב-16:55 מאת ‪Christopher Markiewicz‬‏ <‪<a href="mailto:markiewicz@stanford.edu">markiewicz@stanford.edu</a>‬‏>:‬<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">



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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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<div id="gmail-m_-2017045096526730140divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Neuroimaging <neuroimaging-bounces+markiewicz=<a href="mailto:stanford.edu@python.org" target="_blank">stanford.edu@python.org</a>> on behalf of נתי שטרן <<a href="mailto:nsh531@gmail.com" target="_blank">nsh531@gmail.com</a>><br>
<b>Sent:</b> Friday, July 8, 2022 9:38:57 AM<br>
<b>To:</b> Neuroimaging analysis in Python <<a href="mailto:neuroimaging@python.org" target="_blank">neuroimaging@python.org</a>><br>
<b>Subject:</b> Re: [Neuroimaging] NILEARN - WHY THIS CODE THROWS AN ERROR?????</font>
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<div dir="ltr">it's a fullpath to nifti image </div>
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<div dir="rtl">‫בתאריך יום ו׳, 8 ביולי 2022 ב-16:27 מאת ‪Matthew Brett‬‏ <‪<a href="mailto:matthew.brett@gmail.com" target="_blank">matthew.brett@gmail.com</a>‬‏>:‬<br>
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Hi,<br>
<br>
‪On Fri, Jul 8, 2022 at 2:05 PM ‫נתי שטרן‬‎ <<a href="mailto:nsh531@gmail.com" target="_blank">nsh531@gmail.com</a>> wrote:‬<br>
><br>
> fullcode:<br>
><br>
><br>
><br>
> import nilearn.plotting as plot<br>
> import os,gzip,io<br>
> import nibabel as nib<br>
> path="C:/users/administrator/desktop/nii"<br>
> path2="C:/users/administrator/desktop/nii/out/"<br>
> for i in os.listdir(path):<br>
>     if(".nii.gz" in i):<br>
>         pass<br>
>     else:<br>
><br>
>         if(".nii" in i):<br>
>             img = nib.load(path+"/"+i)<br>
>             data = img.get_fdata()<br>
>             print(data)<br>
>             import imageio<br>
>             X=0<br>
>             for s in data:<br>
>                 import numpy<br>
>                 aleph=numpy.array(s,dtype=numpy.int8)<br>
>                 X=X+1<br>
>                 plot.plot_img(aleph)<br>
><br>
>                 imageio.imwrite("C:\\users\\administrator\\desktop\\nii\\"+i+str(X)+'.jpg', s)<br>
><br>
><br>
><br>
><br>
><br>
><br>
> error:<br>
> Data given cannot be loaded because it is not compatible with nibabel format<br>
<br>
Honestly - I wouldn't email python-list - this is a neuroimaging question.<br>
<br>
The obvious debugging step here is to see what "path+"/"+i" is.  Is it<br>
in fact a filename of a nifti image?  Try loading it in some other<br>
Nifti reader.   If you get stuck, put the file up somewhere where we<br>
can get it and try loading it.<br>
<br>
Cheers,<br>
<br>
Matthew<br>
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