Hi NeuroStars,
I am looking to run some analyses on HCP unprocessed data to test/compare pre-processing methods. I wrote a script to rename/organize the data into BIDS format. Normally, however, when I BIDSify our lab’s data, we convert DICOMs to NIfTIs using dcm2niix, which automatically generates detailed JSONs for each image.
The HCP unprocessed images already come in NIfTIs, so it seems I’ll have to create the JSONs myself based on HCP’s scanning protocol. Personally, this causes two problems for me.
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I’m wondering how info like slice-timing information can be gleaned from these NIfTI files; again, I usually rely on dcm2niix to auto-generate this from the DICOM.
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I am looking to create JSONs for the DWI data (which I am not trained in), and many of the parameters confuse me involving direction/polarity etc. Since probably only a few JSONs can describe the scanning parameters for all the DWI protocols, I’d be shocked if these files haven’t been created before by others. I looked at the BIDS examples page on OpenNeuro, but there were no example HCP datasets with DWI JSONs.
In other words, because of the ubiquity of HCP data, I’m surprised there isn’t a publicly available BIDSified version of the unprocessed data (if there is, and I’m missing it, please please let me know!). Along the same lines, if anyone has made/procured the metadata files or knows somewhere they are uploaded online, I’d be so grateful to access them!
I suppose one alternative would be to get my hands on an HCP DICOM and see what dcm2niix can provide, but I doubt the DICOMs are publicly available.
If it turns out I have to make the JSONs myself, I’d be happy to upload them. That said, I am new to the neuroimaging world, and I’d much rather rely on someone who knows more about what each of the parameters mean.
Thank you!
Brian