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.')^