# 3D Registration of Anatomical and functional MRI of Brain Images

**URL:** <https://discourse.itk.org/t/3d-registration-of-anatomical-and-functional-mri-of-brain-images/6612>\
**Category:** Algorithms\
**Tags:** simpleitk, registration, python\
**Created:** [May 2, 2024, 11:30am UTC](https://discourse.itk.org/t/3d-registration-of-anatomical-and-functional-mri-of-brain-images/6612 "2024-05-02T11:30:20Z")\
**Posts on this page:** 1\
**Showing post:** 17

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**Author:** ![zivy](https://discourse.itk.org/user_avatar/discourse.itk.org/zivy/32/1726_2.png) [@zivy](https://discourse.itk.org/u/zivy)\
**Post date:** [June 6, 2024, 12:59pm UTC](https://discourse.itk.org/t/3d-registration-of-anatomical-and-functional-mri-of-brain-images/6612/17 "2024-06-06T12:59:07Z")

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Hello @debapriya,

You are asking for help without providing relevant details. Just saying I’ver performed registration and “the transformed ROI image is an all black image.” is not a useful description of the problem.  
There could be issues with:

1. Registration failing (converging to a local minimum that is far from the one that aligns the images).
2. Resampling (using the wrong transformation direction or grid definition).
3. Visualization (which you already encountered in [your other question](https://discourse.itk.org/t/nii-image-not-displaying-with-simpleitk-gui/6667)).

You need to confirm success of each sub-step before you can move on to the next step.

Having said this, I will hazard a guess at the issue just based on the images:

The ROI image looks like a contour and not the object itself. When the ROI signal is sparse, high frequency, you will often encounter aliasing when performing resampling. See [this question and guidance](https://discourse.itk.org/t/resample-small-mask/3950) on how to resolve this specific issue.

If this does not address the problem, you will need to provide a more complete description.

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_[View the full topic](https://discourse.itk.org/t/3d-registration-of-anatomical-and-functional-mri-of-brain-images/6612)._