[Neuroimaging] NILEARN - WHY THIS CODE THROWS AN ERROR?????

[Christophe Pallier]

You can pass a filename directly to plot_img (there is no need to use
nibabel, numpy, etc. to extract data).

 Also you can save the figure without imagio, using  savefig() from
matplotlib or even directly from nilearn (see examples in its doc)






On Fri, Jul 8, 2022, 16:35 נתי שטרן <nsh531 at gmail.com> wrote:

> HOW TO DO THIS?
> I'm new in numpy :)
>
> ‫בתאריך יום ו׳, 8 ביולי 2022 ב-16:55 מאת ‪Christopher Markiewicz‬‏ <‪
> markiewicz at stanford.edu‬‏>:‬
>
>> 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>:‬
>>
>> Hi,
>>
>> ‪On Fri, Jul 8, 2022 at 2:05 PM ‫נתי שטרן‬‎ <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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>>
>>
>>
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>
>
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