Atrophy Simulator Developer's Manual
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Atrophy Simulator Package
Contents
[hide]

    * 1 Install
    * 2 Test program
    * 3 File List
    * 4 Links

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Install

Go to the ./src/ folder, and type

make
make install
make clean

then, you get the updated executables in the ./bin/ folder.


The first command "make" compiles all the source codes and generates all the *.o and executables in the folder ./src/. The second command "make install" moves all the executables to the ./bin/ folder, and the third command "make clean" clean up all the temporary files in the ./src/ folder.


After compile all the codes, you need to set your system environment variable to the ./bin/ folder.

for example:

setenv AtrophySimulatorBin /sbia/home/zxue/zxue1/svn/AtrophySimulator/bin/
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Test program

Go to the ./sample/ folder

run command:

${AtrophySimulatorBin}/LinuxSimulateAtrophy.sh jakob_cbq.img jakob_segmented.img 256 256 198 183 107 72 20 .7 sim.field sim.inv.field sim.img sim.seg
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File List

shell programs:
Program	Description
LinuxSimulateAtrophy.sh 	The main program for atrophy simulation
LinuxSimulateAtrophyV2.sh	no use

executables with source:
LinuxDeformationFieldOffsetAbsoluteShift 	deformationfield_offset_absolute_shift.c
LinuxVolumeMatching3D 	VolumeMatching3D.c
LinuxGenerateTargetVolumeBK 	generate_target_volume_bk.c
LinuxRecoverDeformationField 	recover_deformationfield.c
LinuxImageTransformation>	image_transformation.c
LinuxResaveDeformationField 	resave_deformationfield.c

executables without source codes in this distribution:

LinuxTransferDeformationFieldFormat --- deformation field compression program, it is available in other package.

LinuxInverseDeformationField --- reverse deformation field, lab common program. 
