Getting your MRI data

  1. Easiest to do from CBS server (see Servers page), because everything is pre-installed
    • containers for cfmm2tar and tar2bids are located in /srv/containers
  2. Use the Khan lab cfmm2tar tool to download the dicoms from the server
    • Best practice: save the call you’re using in a clearly named file in your project directory (e.g., “run_cfmm2tar.sh”)
    • test with a single date (-d flag) before pulling a whole study
    • use apptainer run /srv/containers/cfmm2tar_<version>.sif -h to get help text, where version is the version number
      • you can check the versions that are available by looking in the /srv/containers directory
    • Example call: apptainer run --bind /cifs/baron/studyData/morrow_ADD/dataTar:/dataTar /srv/containers/cfmm2tar_v1.0.0.sif -p 'Morrow^ADD-MRI' /dataTar
  3. Use the Khan lab “tar2bids” tool to convert the dicoms to NIFTI, organized in the BIDS format
    • Best practice: save the call you’re using in a clearly named file in your project directory (e.g., “run_tar2bids.sh”)
    • call with the no flags for help information. e.g. apptainer run /srv/containers/tar2bids_v0.3.0.sif
    • the rules for naming of files based on the metadata from the scanner can be supplied via a “heuristic” file supplied via the -h option
      • the default one created by the Khan lab will work for most standard scans
        • our advanced diffusion scans will just be given generic dwi names that do not reflect things like b-tensor encoding or ogse
      • if you supply a file, it replaces the default, so you’ll have to redefine the rules for rest of the scans too
        • the heuristic is saved in the “code” directory that is outputted, so you can run tar2bids with the default heuristic in a sample subject, then modify the heuristic file it creates
          • the metadata is saved in a “dicominfo.tsv” file in the same folder, which you can use to create your own rules

Manual download of Dicoms

Go to https://dicom.cfmm.uwo.ca/dm/ and follow the directions.

  • you’ll need to convert to NIFTI for most tools. You can use “dcm2niix” from the command line to do so.
    • check help with dcm2niix -h

Raw Data

  1. Tech will transfer data to the lab’s CBS server allocation. This is mounted on baron1 at /srv/bmisrv_baron
  2. The data will be in the folder “cfmm_data” on our CBS data share, which is at /cifs/bmisrv_baron/cfmm_data on most systems
  3. Move the data from cfmm_data to the appropriate long term storage location (likely a trainee specific folder or studyDataRaw)