Applying N4 bias field correction on TCIA breast DCE-MRI images

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Hi everyone,

I’m trying to do the N4 correction from open-source breast cancer MRI images: Single site breast DCE-MRI data and segmentations from patients undergoing neoadjuvant chemotherapy (Breast-MRI-NACT-Pilot) - The Cancer Imaging Archive (TCIA) Public Access - Cancer Imaging Archive Wiki

These images only show one side of the breast, when I want to do N4 on it by 3D-slicer, I can’t select the volume as input volume in Filtering > N4ITK MRI Bias Correction.
Then I transferred this series of DICOM images into NRRD format, and re-open it but I still couldn’t select it as input volume.

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21144×470 108 KB

Then I tried to do it in python, but with the error:

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31417×513 27.9 KB

Can anyone know how to solve this problem? You can download images from the above links and the “Sagittal-IR_3DFGRE” series was what I used.

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This breast TCIA data set is always very problematic. The main complication is that most images are time sequences.

Most modules will not allow you to select a time sequence as input. If you load the data as “Volume sequence” (using “Advanced” option in the DICOM module) then the current timepoint will show up as a simple scalar volume and so you can run bias correction on it.

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