[Neuroimaging] [nibabel] Issue when saving nifti files

[Ariel Rokem]

Hi Sulantha,

Thanks for getting in touch. Let's see if I can be helpful.

On Fri, Jun 3, 2016 at 7:11 AM, Sulantha Sanjeewa <sulantha.s at gmail.com>
wrote:

> Dear all,
> I am having trouble saving nifti files using nibabel. This is a simple
> load - mask - save situation. However, when I save, the resultant image is
> only two values [min and max] of the original image (almost like a mask).
> Can you help me on this. I have added the code here. and a link to the
> three files as well.
> Thanks a lot for the help.
> Best regards,
> Sulantha.
>
> Files Link: https://drive.google.com/open?id=0B-TWCTRv7UM1a0hxaWotbjRSSUE
> Code:
>
> img = nibabel.load('I300779.nii')
> imgData = img.get_data()
> mask = nibabel.load('FullBrain.nii')
> maskData = mask.get_data()
> maskedImgData = imgData[maskData>0.9]
> new_image = numpy.zeros(maskData.shape)
> new_image[maskData>0.9] = maskedImgData
> aff = mask.affine
> nibabel.save(nibabel.Nifti1Image(new_image, aff), 'I300779_m.nii')
>
>
I am not seeing this when I run your code (
https://gist.github.com/arokem/7f996b56d8f7e17ae8377677314a25ad). I also
find that whole range of values in the file you processed and provided (try
running those two last cells on your file). What are you doing to check the
values in "I300779_m.nii"? Maybe the software reading this file downstream
is doing something funny?

Cheers,

Ariel


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