====== Preprocess Functional (Hallquist pipeline) ======
  * https://github.com/LabNeuroCogDevel/fmri_processing_scripts
  * https://zenodo.org/badge/latestdoi/5274327

Developed by [[https://scholar.google.com/citations?user=mDOXA1wAAAAJ|Michael Hallquist]]

===== Output 4D nifti prefix =====
As the pipeline progresses it outputs files with distinct prefixes that describe each step in reverse order. e.g. final output might be ''brnwsdktm_func_4.nii.gz'' where motion correction was the first preproc step preformed and bandpassing the last.


|''br'' | bandpass and nuisance regresssion (simultaneous to not re-intro noise from one to the other) -- used in resting state|
| ''f'' | high pass filter. used for task (cf. ''b'' full bandpass) |
|''n'' | voxel normliazation (prob to 1000*x/median)|
| ''s'' | smoothing. also prepends the FWHM size to the end (''_4'') |
| ''w'' | warp ("spatial normalization"). likely to MNI 2009c Asym template| 
|''d'' | despike (with wavelets)|
|''k'' | skull strip|
|''t''| slice time correct. usually done at the same time as motion below (via ''4dslicealign.py'')|
|''m'' | motion: realign (6dof affine -- trans and rot) every timepoint to the mean so a voxel is in the same spot over time   |