ON_MR_segmentation_v2_0_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.

• 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>

r4212 | robharrigan | 2016-02-08 11:17:39 -0600 (Mon, 08 Feb 2016) | 1 line

removing nlss files

r4209 | robharrigan | 2016-02-05 15:06:58 -0600 (Fri, 05 Feb 2016) | 1 line

updating upload order

r4195 | robharrigan | 2016-02-04 12:34:39 -0600 (Thu, 04 Feb 2016) | 1 line

renaming resources

r4189 | robharrigan | 2016-02-04 10:11:41 -0600 (Thu, 04 Feb 2016) | 1 line

fixing upload bug...

r4175 | robharrigan | 2016-01-29 12:23:07 -0600 (Fri, 29 Jan 2016) | 1 line

bug fixes with JLF addition

r4168 | robharrigan | 2016-01-28 13:59:50 -0600 (Thu, 28 Jan 2016) | 1 line

adding JLF to spider and processor

r4162 | robharrigan | 2016-01-27 11:44:36 -0600 (Wed, 27 Jan 2016) | 1 line

updating version name and text flushing

r4128 | robharrigan | 2016-01-25 13:54:47 -0600 (Mon, 25 Jan 2016) | 1 line

bug fixes for spider

r4089 | robharrigan | 2016-01-13 17:23:49 -0600 (Wed, 13 Jan 2016) | 1 line

updated niftireg path to add bin

r4080 | robharrigan | 2016-01-12 16:47:35 -0600 (Tue, 12 Jan 2016) | 1 line

initial add of MR segmentation v2 spider

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

July 2016 Robert L Harrigan email / MASI