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Software references

Chris Markiewicz edited this page Oct 9, 2017 · 17 revisions
Tool Link (pref. code) Citation(s)
FreeSurfer https://github.com/freesurfer/freesurfer
recon-all https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all https://doi.org/10.1006/nimg.1998.0395
bbregister & BBR https://doi.org/10.1016/j.neuroimage.2009.06.060
mri_robust_template https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template https://doi.org/10.1016/j.neuroimage.2012.02.084
mri_robust_register https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register http://dx.doi.org/10.1016/j.neuroimage.2010.07.020
ANTs https://github.com/ANTsX/ANTs https://doi.org/10.3389/fninf.2015.00005
antsRegistration http://dx.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://github.com/ANTsX/ANTs/blob/v2.2.0/Scripts/antsBrainExtraction.sh https://doi.org/10.1038/sdata.2015.3
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://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST https://doi.org/10.1109/42.906424
BET https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET https://doi.org/10.1002/hbm.10062
FLIRT https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT_BBR https://doi.org/10.1006/nimg.2002.1132; https://doi.org/10.1016/S1361-8415(01)00036-6
MCFLIRT https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT https://doi.org/10.1006/nimg.2002.1132
SUSAN https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SUSAN https://doi.org/10.1023/A:1007963824710
MELODIC https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC
ICA-AROMA https://github.com/rhr-pruim/ICA-AROMA/ http://www.sciencedirect.com/science/article/pii/S1053811915001822
PRELUDE & FUGUE https://nipype.readthedocs.io/en/latest/interfaces/generated/workflows.dmri/fsl.utils.html#cleanup-edge-pipeline https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide
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://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#computedvars https://arxiv.org/abs/1704.01469 https://doi.org/10.1101/125021
Framewise displacement https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#framewisedisplacement
Other
a/tCompCor http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#compcor https://doi.org/10.1016/j.neuroimage.2007.04.042
phdiff2fmap https://fmriprep.readthedocs.io/en/stable/sdc/estimation.html#fmriprep.workflows.fieldmap.phdiff.phdiff2fmap https://doi.org/10.1006/nimg.2001.1054
nibabel https://github.com/nipy/nibabel/ https://doi.org/10.5281/zenodo.60808
nilearn https://github.com/nilearn/nilearn/ https://doi.org/10.3389/fninf.2014.00014
nipype https://github.com/nipy/nipype/ https://doi.org/10.5281/zenodo.581704
convert3d https://sourceforge.net/projects/c3d/
Graphics
seaborn https://github.com/mwaskom/seaborn https://doi.org/10.5281/zenodo.883859
matplotlib 2.0.0 https://github.com/matplotlib/matplotlib https://doi.org/10.5281/zenodo.248351
cwebp https://developers.google.com/speed/webp/ https://developers.google.com/speed/webp/docs/webp_study https://developers.google.com/speed/webp/docs/webp_lossless_alpha_study
SVGO https://github.com/svg/svgo

Additional references worth considering:

  • HCP pipeline (for GIFTI surface modifications)