====== Resting State Functional MRI ======

===== Data =====

See [[:tools:rest]] for rest "task" descriptions (projector off, eyes open)

Then sorted by BIDS
===== Pre-processing =====

Preprocessing addresses [[:tools:mr_motion]] (registration), slice timing, fieldmap unwarping (susceptibility correction) skull stripping (brain extraction) for warping (spatial normalization). 

A common solution is [[:tools:fmriprep]] on top of [[:tools:BIDS]].


For Habit (as of 2/10/25):

      /Volumes/Hera/Projects/Habit/mr/fmriprep_habitstudy.bash      nipreps/fmriprep:22.0.0

 see fmriprep website to determine specific settings for script and multi-echo processing- [[https://fmriprep.org/en/stable/workflows.html#:~:text=if%20multi-echo%20bold%20data%20is%20supplied%2C%20this%20workflow%20uses]]


===== Post-processing =====

XCP-D
https://xcp-d.readthedocs.io/en/latest/

===== Analysis =====
  * Resting state functional connectivity
  * T1w/T2w intracortical myelination