# Misalignment between Nifti image and mask

**URL:** <https://discourse.slicer.org/t/misalignment-between-nifti-image-and-mask/11507>\
**Category:** Support\
**Created:** [May 12, 2020, 8:13am UTC](https://discourse.slicer.org/t/misalignment-between-nifti-image-and-mask/11507 "2020-05-12T08:13:33Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Bassam](https://avatars.discourse-cdn.com/v4/letter/b/b38774/32.png) [@Bassam](https://discourse.slicer.org/u/Bassam)\
**Post date:** [May 12, 2020, 8:13am UTC](https://discourse.slicer.org/t/misalignment-between-nifti-image-and-mask/11507/1 "2020-05-12T08:13:33Z")

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Hi, Thanks for your kind reply.  
The problem has been sorted out and I successfully uploaded the mask file, but another problem popped up, which misalignment between the structure in the original image (in my case it is the pancreas) and the mask file (segmented pancreas). I pressed apply button for extracting the features, but unfortunately no output features, i think because of that misalignment. I matched the spatial resolution between the image and the mask files, but it did not work.

Please any idea on who to sort this out ? and thanks

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [May 12, 2020, 6:54pm UTC](https://discourse.slicer.org/t/misalignment-between-nifti-image-and-mask/11507/2 "2020-05-12T18:54:31Z")

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Do you load a grayscale image and segmentation from nifti files and they are not aligned?  
Could you please share at least a sample image, but preferably a sample data set? (upload it somewhere and post the link)

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**Author:** ![Bassam](https://avatars.discourse-cdn.com/v4/letter/b/b38774/32.png) [@Bassam](https://discourse.slicer.org/u/Bassam)\
**Post date:** [May 12, 2020, 11:11pm UTC](https://discourse.slicer.org/t/misalignment-between-nifti-image-and-mask/11507/3 "2020-05-12T23:11:36Z")

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The images in DICOM format, while the segmentation in nifti format.

Kindly, the link for the images is:

> <https://github.com/bassamabunahel/Test/blob/master/image.zip>

and for the mask nifti file is:

> <https://github.com/bassamabunahel/Test/blob/master/mask.nii>

Kindly, since the files are big in size, you may need to either click ‘View raw’ or ‘Download’ button to see the attached files.

Kindly, from the attached image file, I used (t1\_vibe\_obl\_d\_Panc\_5mm\_512\_opp) image sequence to create the mask file (segmentation)(nifti file) using ITK snap.

I am using image J to show the mask file, while for the image, MicroDicom is used.

Appreciated