convert enhanced multi-frame DICOMs to legacy single-frame
Most neuroimaging software is slowly implementing support for the enhanced multi-frame format, which has been around for years now and is becoming ubiquitous. However, when there is no option but to use the legacy single-frame format (such as with Nexstim TMS devices, as of August 2024), you can use a conversion tool from dcm4che.
We host this singularity image on Oscar: /oscar/data/bnc/simgs/dcm4che/dcm4che-tools-5.32.0.sif
You can convert a T1 MPRAGE in a few simple steps:
Put your T1 on Oscar (in this example I put it in my data directory)
In a terminal (easiest is via an Open OnDemand desktop session), change directory to wherever your T1.dcm is
Run this command, replacing the blue with the path to your data directory, green with whatever you want your output files to be named, and red with the file name of your enhanced DICOM:
singularity exec -B /path/to/data/directory/ /oscar/data/bnc/simgs/dcm4che/dcm4che-tools-5.32.0.sif emf2sf --out-file sub-999_t1mprage.dcm 1.3.12.2.1107.5.2.43.67050.30000024042614494562600000019-6-1-1bp2iaj.dcm
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