Set Paths
Add the bin directory containing Atropos to the PATH:
- export PATH=$PATH:/ipldev/scratch/eunyokim/src/BRAINS2012Dec/build/bin
Add the build directory to the PYTHONPATH:
- export PYTHONPATH=$PYTHONPATH:your_BRAINSStandAlone-build_dir/NIPYPE
Code
Notes
A new folder in the current working directory called "priors" will be created. It contains renamed copies of all of the input Prior Probability Images in the form of priorProbImages%02d.nii.gz. These are then used as the input in the --initialization flag for the priors.
For example:
--initialization PriorProbabilityImages[10,priors/priorProbImages%02d.nii.gz,0.8,1e-07]
Inputs
Test Directory : /raid0/homes/jforbes/Desktop/test_Atropos/20130130_10priors
Intensity Images
T1_1_fixed.nii.gz
T1_2_fixed.nii.gz
T2_0_fixed.nii.gz
T2_1_fixed.nii.gz
Mask Image
T1_0_roi.nii.gz
Prior Probability Images
priorProbImages02.nii.gz
priorProbImages03.nii.gz
priorProbImages04.nii.gz
priorProbImages05.nii.gz
priorProbImages06.nii.gz
priorProbImages07.nii.gz
priorProbImages08.nii.gz
priorProbImages09.nii.gz
priorProbImages10.nii.gz
Outputs
The output files will be placed in the current working directory.
POSTERIOR_01.nii.gz
POSTERIOR_02.nii.gz
POSTERIOR_03.nii.gz
POSTERIOR_04.nii.gz
POSTERIOR_05.nii.gz
POSTERIOR_06.nii.gz
POSTERIOR_07.nii.gz
POSTERIOR_08.nii.gz
POSTERIOR_09.nii.gz
POSTERIOR_10.nii.gz
T1_0_labeled.nii.gz
priors/
priorProbImages01.nii.gz
priorProbImages02.nii.gz
priorProbImages03.nii.gz
priorProbImages04.nii.gz
priorProbImages05.nii.gz
priorProbImages06.nii.gz
priorProbImages07.nii.gz
priorProbImages08.nii.gz
priorProbImages09.nii.gz
priorProbImages10.nii.gz