How should config look for Tw VNavs ? (getting too many (127) niftis)

1

Hi, I am running dcm2bids on new dataset. Everything looks good but the structural T1 and T2 vNAV sequences are broken up into many runs (assuming that is a quirk of the vNAV sequence that takes the “navigators”). If anyone has guidance on how these should be converted would be much appreciated.

Thanks
NB

VNav_runs
VNav_runs1920×804 255 KB

2

Hi @Sotsub and welcome to neurostars!

Usually for T1w, you only want the RMS mean across the scans. It’s typically the last output of the associated dicoms, with the largest file size.

I don’t know your current config, but chances are you were using just the SeriesDescription. All the T1w files from that scan have the same SeriesDescription so you need additional criteria.

Here is an example of what I have used. Of course, change it as needed for your dicom names, but note the additional ImageType criterion:

    {
            "datatype": "anat",
            "suffix": "T1w",
            "criteria": {
                "SeriesDescription": "T1w_MPRAGE_FourEcho_vNav RMS",
                "ImageType": [
                    "ORIGINAL",
                    "PRIMARY",
                    "OTHER",
                    "ND",
                    "NORM",
                    "MEAN"
                ]
            },
            "custom_entities": "acq-vNav_rec-NORM"
        },

Best,
Steven

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