DicomToNifti_Y dcm2niix Pipeline creates NIFTI files from DICOM files using dcm2niix (modified). Flavin John flavinj@mir.wustl.edu 20180811 scanids xnat:imageSessionData/scans/scan/ID Scan ids of all the scans of the session output_nifti_filename_format %n_%s_%d Filename format ^concat(/Pipeline/parameters/parameter[name='logdir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='label']/values/unique/text())^ workdir ^concat(/Pipeline/parameters/parameter[name='builddir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='label']/values/unique/text())^ logdir ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/LOGS')^ rawdir ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW')^ niidir ^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/NIFTI')^ ^/Pipeline/parameters/parameter[name='rawdir']/values/unique/text()^ ^/Pipeline/parameters/parameter[name='niidir']/values/unique/text()^ ^PIPELINE_LOOPON(series)^ ^fileUtils:getJSESSION('DUMMY')^ GET ^concat('"',/Pipeline/parameters/parameter[name='host']/values/unique/text(),'/data/experiments/',/Pipeline/parameters/parameter[name='id']/values/unique/text(),'/scans/',PIPELINE_LOOPON(series),'/resources/DICOM/files"')^ ^concat(/Pipeline/parameters/parameter[name='rawdir']/values/unique/text(),'/',PIPELINE_LOOPON(series))^ ^PIPELINE_LOOPON(series)^ y y ^/Pipeline/parameters/parameter[name='output_nifti_filename_format']/values/unique/text()^ ^concat(/Pipeline/parameters/parameter[name='niidir']/values/unique/text(),'/',PIPELINE_LOOPON(series))^ ^concat(/Pipeline/parameters/parameter[name='rawdir']/values/unique/text(),'/',PIPELINE_LOOPON(series))^ ^fileUtils:getJSESSION('DUMMY')^ PUT ^concat('"',/Pipeline/parameters/parameter[name='host']/values/unique/text(),'/data/experiments/',/Pipeline/parameters/parameter[name='id']/values/unique/text(),'/scans/',PIPELINE_LOOPON(series),'/resources/NIFTI/files?overwrite=true&format=NIFTI&content=NIFTI_RAW&reference=',/Pipeline/parameters/parameter[name='niidir']/values/unique/text(),'/',PIPELINE_LOOPON(series),'&event_id=',/Pipeline/parameters/parameter[name='workflowid']/values/unique/text(),'"')^