Behavior and Neuroimaging Core User Manual
  • About
  • Infrastructure Overview
  • XNAT
    • Getting Started
    • Accessing XNAT
    • BIDS Ready Protocols
    • New XNAT projects
    • Uploading Data
    • Downloading Data
  • Demo Dataset
    • Introduction
    • How to access it
    • Protocol Information
    • Basic analysis example: checks task
  • XNAT to BIDS
    • Getting Started
    • XNAT2BIDS Software
    • Exporting to BIDS using Oscar
      • Oscar Utility Script
        • Running xnat2bids using default configuration
        • Running xnat2bids with a custom configuration
        • Syncing your XNAT project & Oscar data directory
        • Extra tools & features
      • Step-wise via Interact Session
    • BIDS Validation
      • Oscar
      • Docker
    • Converting non-MR data
      • Physiological data
      • EEG data
  • XNAT TO BIDS (Legacy)
    • Oscar SBATCH Scripts
  • BIDS and BIDS Containers
    • Introduction to BIDS
    • mriqc
    • fmriprep
    • BIDS to NIMH Data Archive (NDA)
  • Analysis Pipelines
    • Freesurfer
    • 🚧CONN Toolbox
    • FSL topup and eddy
    • Tractography: DSI Studio
    • Brown University MRS Data Collection and Preprocessing Protocol
    • LC Model
      • Installation
      • Example Run
      • Running LCModel on your own data
    • Quantitative Susceptibility Mapping (QSM)
  • Standalone Tools
    • Multi-session spectroscopy with voxalign
    • dicomsort: a tool to organize DICOM files
    • ironmap
    • convert enhanced multi-frame DICOMs to legacy single-frame
    • DICOM anonymization
  • MRF GUIDES
    • MRI simulator room
      • Motion Trainer: Balloon Task
      • Simulating scanner triggers
    • Stimulus display & response collection
    • Eyetracking at the scanner
    • Exporting data via scannershare
    • EEG in the scanner
    • Exporting spectroscopy RDA files
  • Community
    • MRF/BNC user community meetings
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  1. Standalone Tools

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:

  1. Put your T1 on Oscar (in this example I put it in my data directory)

  2. In a terminal (easiest is via an Open OnDemand desktop session), change directory to wherever your T1.dcm is

  3. 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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Last updated 8 months ago

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