I am new to MRtrix3 and would like to conduct a whole-brain probabilistic tractography and generate Whole-brain structural connectivity matrices with the output from Freesurfer. I learned from the HCP pipeline that “T1w_acpc_dc_restore_brain.nii.gz” are need for structural preprocessed files. I was wondering what it is? Is it the original T1.nii.gz file?
This is an image that is generated specifically by the HCP structural image pre-processing pipeline, so is not anything specific to MRtrix3. The file name indicates the sequence of processing steps that were performed in the generation of that provided image, which are not likely to be replicated if you are using your own data rather than HCP data.
If by “I learned from the HCP pipeline …” you are referring to this documentation page, please note the warning at the top of the page. Particularly if you are new to MRtrix3 you may be better off instead looking at @martahedl’s BATMAN tutorial.