N4ITK MRI Bias Field Correction input file type?

Support
1

Operating system: macOS Catalina
Slicer version: none
Expected behavior: Output a volume in Nifti format
Actual behavior: none

Hi there, I am new to 3D slicer and was wondering if it’s N4ITK Bias Field Correction module accepted Nifti image files as input. More specifically I plan to run this module on a T1 weighted MPRAGE brain volume in Nifti file format. I was wondering if the module with accept this format and also output a corrected volume in Nifti as well. Additionally, I was wondering if the Bias Field Image output is also output as a volume and what file type is output when using this option.

Thank you for your help,
Stephen

2

Yes, Slicer can read MRI from a Nifti file, apply bias correction, and save result as Nifti file.

3

Thank you so much :slight_smile:
I was able to run it successfully, via command line, generate the bias field, and view it in FSL. It looks wonderful.

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14599×2568 1.32 MB
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24591×2575 1.36 MB
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34588×2585 1.59 MB

4

Great! Check out Slicer’s visualization and processing capabilities, too. We also have a FreeSurfer extension that can import data sets. There are tons of tools that fsleyes does not have - from virtual reality tractography to real-time surgical navigation with BrainLab/StealthStation/custom tracker, advanced image segmentation and surface editing, cutting, etc.

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