Dear PESTICA/SLOMOCO users

The latest version of PESTICA/SLOMOCO expects that the input EPI file includes the correct SMS (MB) slice acquisition timing info. To do it, it is suggested to generate SMS slice timing shift 1D file by running "genSMStimeshift.m", then to inject slice timing shift info when converting dicom to NIFTI file, e.g. using "to3d". In case of already existing nifti file, it is suggested that "3drefit" can be used to inject SMS slice timing info.

However, I found the followings; please reply and correct them if I am wrong
1. 3refit slice timing injection is not working after motion correction and or deoblique.
2. 3refit slice timing injection is only working before motion correction.
3. 3refit/to3d slice timing injection is working not in a nifti format but in a BRIK format of file. (not sure)
4. HCP data is AD-PC aligned (tilted), and motion correction with AC-PC realigned process is applied in the very early stage in pre-processing pipeline.

PESTICA and SLOMOCO should be applied before motion correction and resampling/re-slicing/deoblique. 

The future version of PESTICA/SLOMOCO would have an input option to add slice timing info, which would resolve the problem described above. but keep in mind that PESTICA and SLOMOCO should be applied before motion correction and resampling/re-slicing/deoblique.

Thanks

-Wanyong