{"action":"created","issue":{"url":"https://api.github.com/repos/stnava/ANTs/issues/269","labels_url":"https://api.github.com/repos/stnava/ANTs/issues/269/labels{/name}","comments_url":"https://api.github.com/repos/stnava/ANTs/issues/269/comments","events_url":"https://api.github.com/repos/stnava/ANTs/issues/269/events","html_url":"https://github.com/stnava/ANTs/pull/269","id":126212508,"number":269,"title":"ENH: allows ansCorticalThickness to be called via 5 separate stages","user":{"login":"stnava","id":324222,"avatar_url":"https://avatars.githubusercontent.com/u/324222?v=3","gravatar_id":"","url":"https://api.github.com/users/stnava","html_url":"https://github.com/stnava","followers_url":"https://api.github.com/users/stnava/followers","following_url":"https://api.github.com/users/stnava/following{/other_user}","gists_url":"https://api.github.com/users/stnava/gists{/gist_id}","starred_url":"https://api.github.com/users/stnava/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stnava/subscriptions","organizations_url":"https://api.github.com/users/stnava/orgs","repos_url":"https://api.github.com/users/stnava/repos","events_url":"https://api.github.com/users/stnava/events{/privacy}","received_events_url":"https://api.github.com/users/stnava/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-01-12T16:06:14Z","updated_at":"2016-01-12T20:29:44Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/stnava/ANTs/pulls/269","html_url":"https://github.com/stnava/ANTs/pull/269","diff_url":"https://github.com/stnava/ANTs/pull/269.diff","patch_url":"https://github.com/stnava/ANTs/pull/269.patch"},"body":"allow stages 1 to 5 to be called separately and in order.  this permits finer grained control over the process timing. produces nearly identical results to and is backward compatible with the unstaged antsCorticalThickness.  the test comparison is based on the ants example for antsCorticalThickness:\r\n    \r\n    #!/bin/bash\r\n    DATA_DIR=${PWD}\r\n    TEMPLATE_DIR=${DATA_DIR}/Template/\r\n    OUT_DIR=${DATA_DIR}/OutputT1Only/\r\n    \r\n    bash ${ANTSPATH}antsCorticalThickness.sh -d 2 -x 25 -u 0 \\\r\n      -a ${DATA_DIR}/IXI002-Guys-0828-T1_slice90.nii.gz \\\r\n      -e ${TEMPLATE_DIR}template_slice80.nii.gz \\\r\n      -m ${TEMPLATE_DIR}template_cerebrum_mask_slice80.nii.gz \\\r\n      -p ${TEMPLATE_DIR}prior%d_slice80.nii.gz \\\r\n      -o ${OUT_DIR}example\r\n    \r\n    # test stages\r\n    OUT_DIR=${DATA_DIR}/OutputT1OnlyByStage/\r\n    for stage in 1 2 3 4 5 ; do\r\n      bash ${ANTSPATH}antsCorticalThickness.sh -d 2 -x 25 -u 0 -y $stage \\\r\n        -a ${DATA_DIR}/IXI002-Guys-0828-T1_slice90.nii.gz \\\r\n        -e ${TEMPLATE_DIR}template_slice80.nii.gz \\\r\n        -m ${TEMPLATE_DIR}template_cerebrum_mask_slice80.nii.gz \\\r\n        -p ${TEMPLATE_DIR}prior%d_slice80.nii.gz \\\r\n        -o ${OUT_DIR}example\r\n    done\r\n    \r\nwhich produces (nearly) identical output.  following stages require previous stages to be called."},"comment":{"url":"https://api.github.com/repos/stnava/ANTs/issues/comments/171044980","html_url":"https://github.com/stnava/ANTs/pull/269#issuecomment-171044980","issue_url":"https://api.github.com/repos/stnava/ANTs/issues/269","id":171044980,"user":{"login":"ntustison","id":324811,"avatar_url":"https://avatars.githubusercontent.com/u/324811?v=3","gravatar_id":"","url":"https://api.github.com/users/ntustison","html_url":"https://github.com/ntustison","followers_url":"https://api.github.com/users/ntustison/followers","following_url":"https://api.github.com/users/ntustison/following{/other_user}","gists_url":"https://api.github.com/users/ntustison/gists{/gist_id}","starred_url":"https://api.github.com/users/ntustison/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ntustison/subscriptions","organizations_url":"https://api.github.com/users/ntustison/orgs","repos_url":"https://api.github.com/users/ntustison/repos","events_url":"https://api.github.com/users/ntustison/events{/privacy}","received_events_url":"https://api.github.com/users/ntustison/received_events","type":"User","site_admin":false},"created_at":"2016-01-12T20:29:44Z","updated_at":"2016-01-12T20:29:44Z","body":"Okay, I'll put it in the cortical thickness example later today and then merge it."}}