Dicom send

This is only needed if dicoms are no longer present on the scanner console, but are available somewhere else.

module load dcmtk
storescu -v -xs -aec SC-AMC-01 -aet <MY_AETITLE> apollo.spinozacentre.knaw.nl 6790 --scan-directories --recurse --scan-pattern '*.dcm' <PATH_TO_DICOM_FOLDER>

Using the scanner console name (3T-ACQ, 7T-ACQ, 7T-ACQ-MULTIX) for <MY_AETITLE> ensures the data winds up in the correct folder on the AMC side of things. <PATH_TO_DICOM_FOLDER> is the directory containing the .dcm files (recursive).

It is possible to convert a nifti to enhanced dicom on the minerva command line using xmedcon (https://xmedcon.sourceforge.io/). Dicom headers will be empty though. A subject ID can be added using dcmodify (available in the dcmtk module). See https://support.dcmtk.org/docs/dcmodify.html.