run-pincram

#!/usr/bin/env bash

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# Parallelization architecture / middleware
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PINCRAM_ARCH=bash
# PINCRAM_ARCH=bash-single
# PINCRAM_ARCH=ge
# PINCRAM_ARCH=pbs
export PINCRAM_ARCH
# export PINCRAM_QUEUE=myqueue ## Gets added to qsub call with -q option
# export PINCRAM_CHUNKSIZE=1 ## Number of registrations per array subjob
# export PINCRAM_PBS_OPTION="-l place=free" ## Per-system options


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# Registration library to use
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# Options are mirtk (recommended), greedy (under development), or irtk (deprecated)

export PINCRAM_USE_LIB=mirtk 


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# Execution parameter
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export PINCRAM_PROCEED_PCT=100 ## Minimum % ratio of expected atlas transformations on which to continue
                               ## Trades off reproducibility and accuracy against speed
                               ## Reduce for rapid testing or when jobs are executed unreliably


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# Set search path
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base_sw_path=$HOME/software 

## Required -- pincram
PATH=$base_sw_path/pincram:$PATH

## Required -- https://sourceforge.net/projects/niftyseg/
PATH=$base_sw_path/niftyseg/build/seg-apps:$PATH

## Required -- https://github.com/BioMedIA/MIRTK 
PATH=$base_sw_path/mirtk/install/bin:$PATH

## Optional -- https://github.com/BioMedIA/IRTK 
# PATH=$base_sw_path/irtk/bin:$PATH 

## Optional https://sourceforge.net/projects/niftyseg/
# PATH=$base_sw_path/greedy/build:$PATH  

export PATH LD_LIBRARY_PATH

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# Call pincram
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pincram.sh $1 -result result -atlas atlas