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(),'"')^