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Michał Szczepanik edited this page Jan 10, 2018 · 20 revisions

Welcome to the osirix-bids-output wiki!

How to use

  1. Select the required studies. Click Plugins -> Database -> BIDS Output. The plugin will find all unique sequence names across the studies and list them.

  2. Fill in information telling what each study means.

  • If no suffix is chosen, series with a given name will be omitted during export.
  • If a series with a given name occurs more than once for a given subject (and is not a fieldmap), there are two possibilities:
    • if run label was not specified, run numbers will be automatically generated
    • if run number was specified, a re-start of acquisition will be assumed and all sessions but the last will be discarded.
  • Fieldmaps are currently assumed to come in a form of a phasediff and 2 magnitude images, all with the same series name (this is what we get from our Siemens Trio scanner). A similar logic as above is applied to the triplets of series.
  • Additionally, you can enter the minimum number of images in a bold series. The plugin will ignore bold runs with less than the given number of volumes (may be helpful in discarding re-started epi runs)
  • Click save mapping and continue.

  1. A summary of found series will be presented: Set the path to dcm2niix. If an executable is found at ~/dcm2niix, it will be filled in as default. Set the path to where BIDS root will be located. You can create new directories. Optionally check "Use compression" to write .nii.gz files. Click "Export to BIDS". Wait as DICOMs are copied and dcm2niix is being called.

  2. The output folder has the following directory structure. Dicoms have been sorted into folders (this is performed to simplify dcm2niix calls, the resulting dice folder can be manually erased afterwards).

  3. BIDS folder of a single subject looks as follows. Note that there is some inconsistency within fmap folder and the json files come raw from dcm2niix.

Known limitations

  1. Not all BIDS suffixes and terms are available in the GUI. This should be easiest to fix.
  2. If a series name occurs multiple times for a given subject code, it is assumed to be a case of multiple runs (rather than sessions). To export multiple sessions you have to export them one at a time, specifying session number manually (or use different series names across different sessions).
  3. Field maps are handled only in the case of one phasediff and two magnitude images (based on the Siemens Trio output). Phasediff and magnitude are recognized based on the DICOM ImageType (0008, 0008) tag. Magnitude 1/2 are recognized based on the DICOM EchoTime (0018, 0081) tag, with index 1 assigned to the shorter TE.
  4. For some reason, fieldmap files receive an _e1 / _e2 suffix, which is not part of BIDS specification, during dcm2niix conversion.
  5. The json sidecars are raw dcm2niix output. They have to be edited separately to fully conform with BIDS specification.
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