If you have some recommendation regarding HCP-pipline it will be great! (for the unprocessed data)
In what stage do you average between RL and LR scans?
In what stage do you concatenate between the different scans of each subject (3 different gradient tables: 95,96,97).
Furthermore, there is currently release of 35 subjects scanned in MGH Adult Diffusion
MGH Adult Diffusion Data
Minimum data preprocessing:
Gradient nonlinearity correction.
Eddy current correction.
What is the equivalent to gradient nonlinearity correction in mrtrix?
Do you recommend to apply also dwidenoise and mrdegibbs?
Is it possible also with mrtrix first to do Motion correction and then Eddy current correction?
The b=0 images interspersed throughout the diffusion scans were used to estimate the bulk head motions with respect to the initial time point (first b=0 image), where the rigid transformation were calculated with the boundary based registration tool in the FreeSurfer package V5.3.0 (Greve and Fischl, 2009). For each b=0 image, this transformation was then applied to itself and the following 13 diffusion weighted images to correct for head motions. After motion correction, the b-vectors were adjusted according to the rigid rotation estimated.