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Algorithm (0.0.7): TO DO (http://www.ncbi.nlm.nih.gov/pubmed/20851191, http://www.ncbi.nlm.nih.gov/pubmed/19818860)

Version tracking:

0.0.2 >>>
Call: antsMultivariateTemplateConstruction.sh -d 3 -o "${OutDir}/" -n 0 -c 2 -j 2 ${OutDir}/tmp_subjlist.csv

0.0.3 >>> set -y to 0
Call: antsMultivariateTemplateConstruction.sh -d 3 -o "${OutDir}/" -n 0 -i 8 -y 0 -c 2 -j 2 ${OutDir}/tmp_subjlist.csv

0.0.4 >>> rigid registration, increase -m, normalize intensities, pad image, set -y to 0
Call: antsMultivariateTemplateConstruction.sh -d 3 -o "${OutDir}/" -r 1 -n 0 -m 40x60x30 -i 5 -y 0 -c 2 -j 2 ${OutDir}/tmp_subjlist.csv

0.0.5 >>> Skull-stripped, rigid registration, increase -m, normalize intensities, pad image, set -y to 0
Call: antsMultivariateTemplateConstruction.sh -d 3 -o "${OutDir}/" -r 1 -n 0 -m 40x60x30 -i 5 -y 0 -c 2 -j 2 ${OutDir}/tmp_subjlist.csv

0.0.6 >>> Skull-stripped, rigid registration, increase -m, normalize intensities, pad image, set -y to 0, CC radius from 5 to 3
Call: /scripts/antsMultivariateTemplateConstruction.sh -d 3 -o "${OutDir}/" -r 1 -n 0 -m 40x60x30 -i 5 -y 0 ${OutDir}/tmp_subjlist.csv

0.0.7 >>> No skull-strip, one image as reference (no rigid), increase -m, normalize intensities, pad image, CC radius from 5 to 3, get rid of multithreading
Call: /scripts/antsMultivariateTemplateConstruction.sh -d 3 -o "${OutDir}/" -n 0 -m 40x60x30 -i 5 -c 0 -z ${image} ${OutDir}/tmp_subjlist.csv