N4ITK MRI Bias Field Correction input file type?

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,

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

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.

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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