Tool (Package) Citation(s) Link to code or documentation FreeSurfer https://github.com/freesurfer/freesurfer recon-all https://doi.org/10.1006/nimg.1998.0395 https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all bbregister & BBR https://doi.org/10.1016/j.neuroimage.2009.06.060 mri_robust_template https://doi.org/10.1016/j.neuroimage.2012.02.084 https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template mri_robust_register https://doi.org/10.1016/j.neuroimage.2010.07.020 https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register mris_expand https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-July/011152.html ANTs https://doi.org/10.3389/fninf.2015.00005 https://github.com/ANTsX/ANTs antsRegistration https://doi.org/10.1016/j.media.2007.06.004 https://doi.org/10.1016/j.neuroimage.2010.09.025 N4BiasFieldCorrection https://doi.org/10.1109/TMI.2010.2046908 antsBrainExtraction.sh https://doi.org/10.1038/sdata.2015.3 https://github.com/ANTsX/ANTs/blob/v2.2.0/Scripts/antsBrainExtraction.sh FSL https://doi.org/10.1016/j.neuroimage.2004.07.051 https://doi.org/10.1016/j.neuroimage.2008.10.055 https://doi.org/10.1016/j.neuroimage.2011.09.015 FAST https://doi.org/10.1109/42.906424 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST BET https://doi.org/10.1002/hbm.10062 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET FLIRT https://doi.org/10.1006/nimg.2002.1132 https://doi.org/10.1016/S1361-8415(01)00036-6 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT_BBR MCFLIRT https://doi.org/10.1006/nimg.2002.1132 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT SUSAN https://doi.org/10.1023/A:1007963824710 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SUSAN MELODIC https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC ICA-AROMA http://www.sciencedirect.com/science/article/pii/S1053811915001822 https://github.com/rhr-pruim/ICA-AROMA/ PRELUDE & FUGUE https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide https://nipype.readthedocs.io/en/latest/interfaces/generated/workflows.dmri/fsl.utils.html#cleanup-edge-pipeline AFNI https://doi.org/10.1006/cbmr.1996.0014; https://doi.org/10.1016/j.neuroimage.2011.08.056 3dvolreg https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html 3dTshift https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTshift.html 3dUnifize https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dUnifize.html 3dAutomask https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dAutomask.html Power, et al. (2012) measures https://doi.org/10.1016/j.neuroimage.2011.10.018 DVARS https://arxiv.org/abs/1704.01469 https://doi.org/10.1101/125021 https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#computedvars Framewise displacement https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#framewisedisplacement Other a/tCompCor https://doi.org/10.1016/j.neuroimage.2007.04.042 http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#compcor phdiff2fmap https://doi.org/10.1006/nimg.2001.1054 https://fmriprep.readthedocs.io/en/stable/sdc/estimation.html#fmriprep.interfaces.fmap.phdiff2fmap nibabel https://doi.org/10.5281/zenodo.60808 https://github.com/nipy/nibabel/ nilearn https://doi.org/10.3389/fninf.2014.00014 https://github.com/nilearn/nilearn/ nipype https://doi.org/10.3389/fninf.2011.00013 https://doi.org/10.5281/zenodo.581704 https://github.com/nipy/nipype/ convert3d https://sourceforge.net/projects/c3d/ Graphics seaborn https://doi.org/10.5281/zenodo.883859 https://github.com/mwaskom/seaborn matplotlib 2.0.0 https://doi.org/10.5281/zenodo.248351 https://github.com/matplotlib/matplotlib cwebp https://developers.google.com/speed/webp/docs/webp_study https://developers.google.com/speed/webp/docs/webp_lossless_alpha_study https://developers.google.com/speed/webp/ SVGO https://github.com/svg/svgo