Single Echo

[mitchellxh]

Hi!

Thanks for publishing this pipeline! I'd like to adapt this to a single echo dataset. Is that possible and/or how difficult will that be to implement?

[wtsyeda]

Hi,

Thank you for your interest in using our pipeline!

Currently, QSMART pipeline uses multiecho data for coil combination and total field shifts (tfs) estimation (including a voxel reliability map from echo-fitting). Technically, the spatial dependent filtering can be perform on any tfs image (even the one arising from a single echo data) and an externally provided voxel reliability map (can be replaced by a brain mask if all brain voxels are reliable) to estimate the local field shifts (see code lines: https://tinyurl.com/2p8rfu3c and https://tinyurl.com/2p89vutu). So you will need to bypass the coil combination and echofitting steps in the pipeline. I'd recommend setting up a separate pipeline and using QSMART_SDF.m function for estimating the local field shifts followed by iLSQR to obtain QSM images from single echo data. I hope this explanation helps, please let me know if further clarification is needed.

Kind regards,

Warda