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Software at CIS : lddmm-volume : Validation

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Content

Overview

The LDDMM Validation section provides input data, processing and visualization examples for LDDMM to ensure correctness of the resultant data. These examples are useful tests when LDDMM is run on new environments or platforms. Example images show atlas volume in red. On the left, the original target is in grey. On the right, the deformed atlas is pictured. A sample LDDMM command is posted with each example (click here or type ${LDDMM_HOME}/lddmm --help for more LDDMM usage information).

Environment Variables

The LDDMM application requires that two variables be set. Within CIS, there are two configurations.

Linux Desktop
LDDMM_TMP=/tmp
LDDMM_HOME=/cis/project/software/lddmm-volume
Rock Cluster
LDDMM_TMP=/state/partition1/tmp
LDDMM_HOME=/opt/lddmm/1.0.0

Sphere Test

Deforming Sphere Input (64x64x64) in tar+gzip format : A sphere expanding outward evenly in all directions.

Output in tar+gzip format (100 MB)

${LDDMM_HOME}/lddmm -A Ball3D_1.img -T Ball3D_2.img

Original Deformed

L Shape Test

Deforming "L" Version 1 Input (64x64x64) in tar+gzip format : "L" shape expanding in 2 dimensions

Output in tar+gzip format (140 MB)

MayaVi visualization in mv format (included in Output tar file)

${LDDMM_HOME}/lddmm -A littleL.img -T bigL.img

Original Deformed




Deforming "L" Version 2 Input (64x64x64) in tar+gzip format : "L" shape extending in 1 direction

Output in tar+gzip format (133 MB)

${LDDMM_HOME}/lddmm -A littleL.img -T bigL.img

Original Deformed

2d Monkey Brain Test

2-D Monkey Brain Input (80x80) in tar format.

Output in tar+gzip format (3.5 MB)

${LDDMM_HOME}/lddmm -d 2 -A monkey1_80_80.img -T monkey2_80_80.img

Atlas Target
  Deformed Atlas
 

With Velocity vectors (visualized with MayaVi)

Click image for larger picture

Last Modified: Thursday, 30th May, 2013 @ 09:26am

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