Convert DICOMDIR to BIDS

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1

Hello all,

I have MRI data from a Philips scanner that was exported in DICOMDIR structure. This means I have a DICOMDIR file and a folder containing all dicom files. I wish to convert these files to BIDS - I have tried bidskit but with no success.

Do you know any option to perform this conversion?

Thank you in advance!

2

Hi @asayal, have you had a look at HeuDiConv? It wraps dcm2niix, but takes a little bit of Python programming to fully translate files to BIDS.

For future studies, you can talk to your techs about ReproIn to name your DICOMs in such a way that HeuDiConv can run with zero configuration.

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Hi @effigies,

Thank you for your fast reply. I will take a look at HeuDiConv.

I actually found out that bidskit can also handle the DICOMDIR files… I found that the SequenceName field in these DICOM headers was empty, which lead to the misidentification of the sequence names by dcm2niix. However, the ProtocolName field is not empty.

All I had to do was to change the dcm2niix call, by modifying the file output format from
'-f %n--%d--%q--%s'
to
'-f %n--%p--%q--%s'.

Best,

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