Study Setup

• Get study documentation from MRI Centre / PI / RA

  • A list of expected scan types is needed, which will be added to the project settings file
  • The FTP username and password is needed, as well as the name of the folder associated with the project on the MR FTP server
  • If the naming convention of the scans on the MR server differs from the lab's, you will need to obtain a mapping
    • You can check how scans are named by running datman's archive-manifest.py on a scan, and seeing if the PatientName follows the proper convention, if not, request a mapping (or generate one; see "Configuration")

• Configuration

• Add a key-value pair under Projects in /archive/code/config/tigrlab_config.yaml with this format: <project>: <project>_settings.yml

• Create /archive/code/config/<project>_settings.yml, and fill out all project information

  • This involves knowing the study name, description, PI, and scan types (which you obtained above)
  • Look at settings files for other projects for examples of how to format the expected scan types correctly

• Create /archive/code/config/<project>_management.sh; you can copy this from another project, and just need to change the STUDYNAME=<project> line

• Most project directories will be created for you automatically, but you must create /archive/data//metadata

  • Within the metadata directory, create a scans.csv file. This is a space-delimited file, mapping each subject's name in the DICOM header with a name that follows the TIGRLab naming convention. The first line of this file should read: source_name target_name dicom_PatientName dicom_StudyID. Each subsequent line should follow this format: <name of archive file, minus file extension> <subject name, following TIGRLab convention> <PatientName field in DICOM header> <StudyID field in DICOM header>.
  • If you were provided this mapping from the people responsible for the study, copy and paste it here (editing to follow the format, as necessary)
  • If you were not provided this, a tool was created to generate this automatically. However, it is NOT 100% accurate in all cases (for example, it assumes two sessions with the same PatientName are two different timepoints (with the newest session being "timepoint 2"), when it might actually represent a "repeat"). When it doubt, always check with those responsible for the study.
  • The tool is found at /archive/code/datman/datman/generate_scanslist.py, with the following usage: generate_scanslist.py <archive_dir> <study_name> <site_name>. It will output a scans.csv file in the current directory.

• XNAT

• Create new study in XNAT, using same <project> name

• Ensure "clevis" is given ownership of the new study - this is necessary for automatic upload of data from the MR server

• REDCap

  • Add study name and RA name(s) to 'Scan Completed' survey

• Dashboard

  • To add the new study, run the add_study_info.py script (once the settings file exists):
    • $module load /archive/code/dashboard
    • $/archive/code/dashboard/add_study_info.py

• Restart webserver

  • In order for session pages to be viewed on the Dashboard, the webserver must be restarted (this appears to be a caching issue involving the Dashboard reading an old tigrlab_config.yaml file if not restarted)

• Getting the data

  • Unless you have admin privileges, you will need to wait for the nightly run scripts to fetch the data and ensure everything was set-up properly. Come back tomorrow, and ensure all data is in the <project>/data folder, all QC pages are generated in <project>/qc, and all data was uploaded to XNAT. If there were any problems, look at the project-specific logfile in /archive/logs to try to diagnose what went wrong.

Once the data is on our system...

• QC training:

  • A GitHub account must be created for all RAs associated with the study (if they don't have one yet)
  • A Dashboard admin must give the RAs permissions to access the new study

• Gold Standards:

  • Put the first subject in /metadata/standards

The study should now be fully set up. Congratulations!