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tools:rsfmri [2024/11/09 11:39] – created willtools:rsfmri [2025/07/21 11:49] (current) – [Pre-processing] will
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 See [[:tools:rest]] for rest "task" descriptions (projector off, eyes open) See [[:tools:rest]] for rest "task" descriptions (projector off, eyes open)
  
-===== Analysis =====+Then sorted by BIDS 
 +===== Pre-processing =====
  
-TODO: nuisance regression, connectivity analysis+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