DBP3:Utah:RegSegPipeline

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The CARMA DBP: MRI-based study and treatment of atrial fibrillation

Pilot Studies on a Registration & Segmentation Pipeline & Workflow

Overall processing steps are (order tentative)

1. N4 bias field correction for the MRI (surface coils):
   1. run on entire image gives some benefit that may be improved with masking: again the dominant intensity dropoff from the surface coil occurs along the chest wall and ribcage. Even if that is not the structure of interest, it is the low-freq. variation the bias correction algorithm is searching for, and masking that out can be counter-productive: via masking we may end up with a smoother image, but the intensity variations removed were not caused by the coil but are actually true signal.
   2. Module used: N4 ITK
2. registration MRA>cMRI
   1. the MRA contains the same FOV and has surrounding structures (liver, chest, spine etc) visible also, despite lower intensities. A global affine is thus not necessarily going to benefit from masking the heart, unless the relative motion of the heart becomes the dominant reason for misalignment.
   2. Module used: BRAINSfit
3. ROI definition (manual box ROI or automated via atlas)
4. segmentation of LA from MRA -> inner wall
   1. as a dynamic image the MRA contains significant spread and likely requires interactive segmentation/thresholding to yield a satisfactory LA volume
   2. Module used: Editor: thresholding or thresholding within Volumes thresholding option within Display tab, use iron colormap & low alpha setting to check for ventricular wall borders.

1. 1. cropping and island removal
2. LA wall segmentation
   1. very small structure, most reliably done manually direct. Starting with automation may yield more effort on post-edits
3. segmentation of enhancement within LA wall: intensity statistics. An atlas-based set of intensity distributions may be more meaningful here than a simple Otsu, because both amount and location of enhancement is unknown and can in theory be 0.
4. registration follow-up -> baseline
   1. most reliably done on the post contrast MRI.
   2. DOF of 12 or even low-res BSpline should be ok

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  Example contrast MRI with thresholded MRA as color overlay

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  Example contrast MRI with thresholded MRA as color overlay and areas of enhancement marked