ON_MR_segmentation_v2_1_0

• What does it do?

More flexible version of ON_MR_segmentation which utilizes an atlas definition file to allow for multiple atlases to be used to segment a single project. Each scan type is assigned an atlas directory which is used for multi-atlas segmentation on a cropped region. Cropping is done through a rigid multi-atlas segmentation of the eye globes and padding.

v2.1 update allows for rerunning of assessors without repeating registrations. The spider checks for the NON_RIGID_REGISTRATION and CROPPED_TARGETS resources and if they are available, uses them. The process will rewarp all of the atlas labels. This is useful for rerunning segmentations with new label sets. Note that a full rerun is possible by deleting all current resources and restarting the process.

• Requirements

masimatlab utilities

ANTS registration

niftyreg

fsl v5.0

mipav v7.0+

JIST

PICSL MALF jointfusion

• Resources

OUTLOG - STDOUT and STDERR from the process on the grid

PBS - The DRMAA compliant batch script to run the job

PDF - The output PDF file for determining QA status

SNAPSHOTS - Thumbnail of the first page of the PDF resource for viewing on XNAT

JLF - The joint label fusion label result

NLSS - The NLSS label fusion result

targets - The cropped image and a mat file with cropping bounds

non_rigid_registration - The warp and affine transformation outputs from ANTS

MATLAB - The matlab script used to run the segmentation

• References
• Version History

<revision> <name> <date> <lines changed>

Current Contact Person <date> <name> <email / URL>

July 2016 Robert L Harrigan email / MASI