missing JSON files for T1

[Maria Kharitonova]

Hi, I am attempting to convert a subset of ADNI data (N=20 for now) to BIDS using your converter. While I am getting the output I expect, I am not getting .json sidecar files for the T1 images. It converts the data to NIfTI but does not create the json files. I am seeing them for the other modalities (e.g. FLAIR). 

I am using dcm2niix v1.0.20241211 and clinica, version 0.9.3. 

It runs but does not cleanly exit because it cannot find adas_Q1 in the adni_metadata, which I assume is an unrelated issue? 

thank you in advance for your guidance. 

Best,

Maria Kharitonova

[Alice Joubert]

Hello Maria,

Thanks for reporting. 

The json sidecar file is indeed not produced by our ADNI converter for T1 (as well as any PET) modality. I am unsure as to why it is this way, though if you want to try getting them you can modify the following function, line 1019 of file clinica/converters/adni_to_bids/_utils.py : 

```

def _write_json_sidecar(modality: ADNIModalityConverter) -> bool:
    if modality == ADNIModalityConverter.T1:
        return False --> True
    if modality == ADNIModalityConverter.DWI:
        return True
    if modality == ADNIModalityConverter.FLAIR:
        return True
    if modality == ADNIModalityConverter.FMRI:
        return True
    if modality == ADNIModalityConverter.FMAP:
        return True
    if modality in (
        ADNIModalityConverter.PET_FDG,
        ADNIModalityConverter.PET_FDG_UNIFORM,
        ADNIModalityConverter.PET_PIB,
        ADNIModalityConverter.PET_AV45,
        ADNIModalityConverter.PET_TAU,
    ):
        return False

```

You would need to re-run the converter on your subset to a new folder if you want to have them.

The issue with adas_Q1 is indeed unrelated to json files.

Hope this helps,

Alice

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