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[ENH] Add a summary of the important imaging parameters found in input data

Open mattcieslak opened this issue 3 years ago • 2 comments

I think it could be useful to have a TSV in the output that summarizes important parameters in the input datasets and describes how they are included in the results. Potentially something like:

BIDSFile PhaseEncodingDirection PartialFourier TotalReadoutTime SamplingSchemeType FinalFile
sub-X_ses-Y_dwi.nii.gz [ijk-] [float] [float] {"shelled", "cartesian", "random"} sub-X_ses-Y_desc-preproc_dwi.nii.gz

Some background: we have a new Gibbs unringing method in the next release that specifically works with partial fourier acquisitions. If a user selects --combine-before-denoising we need to determine what partial fourier value to set for the combined scan (maybe exit with an error). So a table like this will need to be made during the pipeline building anyways.

Also, since it would be written to the outputs before the pipeline is run it could provide some hints about possible BIDS issues.

Any thoughts on this idea @cookpa @smeisler @tsalo @arokem

mattcieslak avatar Nov 18 '22 14:11 mattcieslak

I think this is a good idea, but it might also be good if these were included in the final *preproc_dwi.json files too if they are not already, since that way these fields could be used in BIDS loader filters. I’m not sure I see the immediate need to filter based on these, but still good to have the option. Not sure if that would require an extension of the DWI BIDS specification.

smeisler avatar Nov 18 '22 15:11 smeisler

I'm thinking this file will go into the DWI Derivatives - is there an official spec for that?

mattcieslak avatar Nov 18 '22 15:11 mattcieslak