Hi,
For --output-resolution, I was wondering if the wrong choice of downsampling will have a negative impact on the pre-processing or subsequent analysis? Does it is necessary to rerun the QSIprep?
Hi Jing_y, The downsampling only happens at the very end of preprocessing, so it won’t affect the earlier parts of the pipeline. The voxel size of your preprocessed data can have effects on things like tractography.