Preprocess Functional (Hallquist pipeline)
Developed by 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 |
QC
See qa_images/ for func overlay on T1w (“mprage”). For full 3D/volumetric images, use qa_images/funct_to_struct.nii.gz with mprage.nii.gz, likely with AFNI GUI's overlay/underlay slider (push 4 or 5).
Existing QC: Quality Checking for Brain Mechanisms R01 (7T) in 7T MR Quality Check