qmenta/mrtrix3_connectome repository overview

Due to use of the Anatomically-Constrained Tractography (ACT) framework, correction of EPI susceptibility distortions is a prerequisite for this pipeline. Currently, this is only possible within this pipeline through use of the FSL tool topup, which relies on the presence of spin-echo EPI images with differences in phase encoding to estimate the causative inhomogeneity field. In the absence of such data, this pipeline is not currently applicable; though recommendations for alternative mechanisms for such correction in the Issues page are welcome, and development of novel techniques for performing this correction are additionally underway.

While many common DICOM conversion software are capable of providing data characterising the phase and slice encoding performed in the acquisition protocol, which are subsequently used by this pipeline to automate DWI data pre-processing, for some softwares and/or some data (particularly those not acquired on a Siemens platform), such data may not be present in the sidecar JSON files for files in the BIDS dwi/ and fmap/ directories. In this circumstance, it will be necessary for users to manually enter the relevant information into these files in order for this script to be capable of processing the data. Every JSON file in these two directories should contain the BIDS fields PhaseEncodingDirection and TotalReadoutTime. For DWI data, it is also preferable to provide the SliceEncodingDirection and SliceTiming fields. More information on these data can be found in the BIDS documentation.