1. RESTAPI Basic Operation Manual
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curl -u username "https://xnat.sydney.edu.au/data/archive/projects/PTV000[insert project name here]/subjects/Haofei01[insert subject name here]/experiments/Haofei01_MR1[insert session name here]/scans/4[insert scan ID here]/files?format=xml" -o filelist.xml
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curl -u username "https://xnat.sydney.edu.au/data/archive/projects/PTV000[insert project name here]/subjects/Haofei01[insert subject name here]/experiments/Haofei01_MR1[insert session name here]/scans/4/DICOM[insert scan id here]/files?format=zip" -o dicomfiles.zip
Note: In this above example, PVT000 is the project name, Haofei01 is the subject name, "Haofei01_MRI" is the session/experiment name, "4" is the scan name.
Upload all files into the scan
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For example, below command downloads to dicomfiles.zip that contains all files for existing scan "3980" of existing session "29", that is for existing subject "MH_Brain" of existing project "fang1".
curl -u xufang "https://dev.xnat.sydney.edu.au/data
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Note: In this above example, PVT000 is the project name, Haofei01 is the subject name, "Haofei01_MRI" is the session/experiment name, "4" is the scan name, "ABC" is the subfolder name, and "files" are necessary to be added.
Create folder
curl -u username o dicomfiles.zip
Upload all files into the scan
curl -u username -X PUT "https://xnat.sydney.edu.au/data/projects/[insert project name here]/subjects/[insert subject name here]/experiments/[insert session name here]/scans/[insert scan id here]/resources/[insert a custom folder name here]/files?extract=true" -F “file=@compresses-file.zip”
For example, below command will decompress test.zip and save all DICOM files into "TEST" folder under existing scan "3980" of existing session "29", that is for existing subject "MH_Brain" of existing project "fang1". You can specify the name of folder, if not existed, it'll be created.
curl -u xufang -X PUT "https://dev.xnat.sydney.edu.au/data/projects/fang1/subjects/MH_Brain/experiments/29/scans/3980/resources/TEST/files?extract=true" -F "file=@test.zip"
Create folder
curl -u username -X PUT "https://xnat.sydney.edu.au/data/projects/[insert project name here]/subjects/[insert subject name here]/experiments/[insert session name here]/scans/[insert scan id here]/resources/[insert a custom folder name here]"
For example, below command creates a sub-folder "TEST3" under scan named "3980" of existing session "29", that is for existing subject "MH_Brain" of existing project "fang1". Note that no further sub-directories are allowed.
curl -u xufang -X PUT "https://xnat.sydney.edu.au/data
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2. How can we determine the project, subject, session/experiments, scan name via the XNAT Web Interface ?
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Step 3. Create the Artemis Scripts
For information about Artemis Job Submission, monitoring and management, please refer to the information page about Artemis.
https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/190284213/Job+Submission
https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/213090348/Job+Monitoring+and+Management
[unikey@login2 ~]$ vi run.pbs
#!/bin/bash
#PBS -P SASTEST
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