DicomToNiftiCconverter /Library/Pipeline_engine/mriconvert Demo pipeline created NIFTI files from the DICOM files and addes these files at SCAN level Mohana Ramaratnam 1 scanids adir:MRExperiment/scans/scan/ID The scan ids of all the scans of the session xnat_id adir:MRExperiment/ID The scan ids of all the scans of the session sessionId adir:MRExperiment/label The scan ids of all the scans of the session project adir:MRExperiment/project Project subject adir:MRExperiment/subject_ID Subject ID ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/DicomToNifti')^ mailhost artsci.wustl.edu workdir ^concat(/Pipeline/parameters/parameter[name='builddir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text())^ NIFTI ^PIPELINE_LOOPON(series)^ RAW ^/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text()^ ^PIPELINE_LOOPON(series)^ ^/Pipeline/parameters/parameter[name='host']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='user']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^ ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW')^ true ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/NIFTI/',PIPELINE_LOOPON(series))^ nifti ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/SCANS/',PIPELINE_LOOPON(series),'/DICOM')^ ^/Pipeline/parameters/parameter[name='user']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='host']/values/unique/text()^ PUT ^concat('"/REST/projects/',/Pipeline/parameters/parameter[name='project']/values/unique/text(),'/subjects/',/Pipeline/parameters/parameter[name='subject']/values/unique/text(),'/experiments/',/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text(),'/scans/',PIPELINE_LOOPON(series),'resources/NIFTI/files/',PIPELINE_LOOPON(series),'.nii?format=NIFTI&content=NIFTI_RAW"')^ ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/NIFTI/',PIPELINE_LOOPON(series),'/*.nii')^ ^/Pipeline/parameters/parameter[name='useremail']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='adminemail']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='adminemail']/values/unique/text()^ ^concat(/Pipeline/parameters/parameter[name='xnatserver']/values/unique/text(), ' update: NIFTI files generated for ',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text() )^ ^/Pipeline/parameters/parameter[name='mailhost']/values/unique/text()^ ^concat('Dear ',/Pipeline/parameters/parameter[name='userfullname']/values/unique/text(),',<br> <p>', ' NIFTI files have been generated for ', /Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),' . Details of the session are available <a href="',/Pipeline/parameters/parameter[name='host']/values/unique/text(),'/app/action/DisplayItemAction/search_element/adir:MRExperiment/search_field/adir:MRExperiment.ID/search_value/',/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text(),'">', ' here. </a> </p><br>', ' </p><br>', 'XNAT Team.')^