Andersson, J. L., Jenkinson, M., & Smith, S. (2007). Non-linear registration, aka Spatial normalisation FMRIB technical report TR07JA2. FMRIB Analysis Group of the University of Oxford, 2(1), e21. http://fsl.fmrib.ox.ac.uk/analysis/techrep/tr07ja2/tr07ja2.pdf

Antonopoulos, G., More, S., Raimondo, F., Eickhoff, S. B., Hoffstaedter, F., & Patil, K. R. (2023). A systematic comparison of VBM pipelines and their application to age prediction. Neuroimage, 279, 120292. https://doi.org/10.1016/j.neuroimage.2023.120292

Article  PubMed  Google Scholar 

Avants, B. B., Tustison, N. J., Song, G., Cook, P. A., Klein, A., & Gee, J. C. (2011). A reproducible evaluation of ants similarity metric performance in brain image registration. Neuroimage, 54(3), 2033–2044. https://doi.org/10.1016/j.neuroimage.2010.09.025

Article  PubMed  Google Scholar 

Boesen, K., Rehm, K., Schaper, K., Stoltzner, S., Woods, R., Luders, E., & Rottenberg, D. (2004). Quantitative comparison of four brain extraction algorithms. Neuroimage, 22(3), 1255–1261. https://doi.org/10.1016/j.neuroimage.2004.03.010

Article  PubMed  Google Scholar 

Coalson, T. S., Van Essen, D. C., & Glasser, M. F. (2018). The impact of traditional neuroimaging methods on the Spatial localization of cortical areas. Proc Natl Acad Sci U S A, 115(27), E6356–E6365. https://doi.org/10.1073/pnas.1801582115

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cox, R. W. (1996). AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29(3), 162–173. https://doi.org/10.1006/cbmr.1996.0014

Article  CAS  PubMed  Google Scholar 

Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., Buckner, R. L., Dale, A. M., Maguire, R. P., & Hyman, B. T. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage, 31(3), 968–980.

Article  PubMed  Google Scholar 

Dickie, E. W., Anticevic, A., Smith, D. E., Coalson, T. S., Manogaran, M., Calarco, N., Viviano, J. D., Glasser, M. F., Van Essen, D. C., & Voineskos, A. N. (2019). Ciftify: A framework for surface-based analysis of legacy MR acquisitions. Neuroimage, 197, 818–826.

Article  PubMed  Google Scholar 

Dubois, J., & Adolphs, R. (2016). Building a science of individual differences from fMRI. Trends in Cognitive Sciences, 20(6), 425–443. https://doi.org/10.1016/j.tics.2016.03.014

Article  PubMed  PubMed Central  Google Scholar 

Eickhoff, S. B., Paus, T., Caspers, S., Grosbras, M. H., Evans, A. C., Zilles, K., & Amunts, K. (2007). Assignment of functional activations to probabilistic cytoarchitectonic areas revisited. [Review]. Neuroimage, 36(3), 511–521. https://doi.org/10.1016/j.neuroimage.2007.03.060

Article  PubMed  Google Scholar 

Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A. I., Erramuzpe, A., Kent, J. D., Goncalves, M., DuPre, E., & Snyder, M. (2019). fMRIPrep: A robust preprocessing pipeline for functional MRI. Nature Methods, 16(1), 111–116.

Article  CAS  PubMed  Google Scholar 

Faul, F., Erdfelder, E., Lang, A. G., & Buchner, A. (2007). G* power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behavior Research Methods, 39(2), 175–191.

Article  PubMed  Google Scholar 

Fischl, B., & Dale, A. M. (2000). Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proceedings of the National Academy of Sciences, 97(20), 11050–11055.

Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., Van Der Kouwe, A., Killiany, R., Kennedy, D., & Klaveness, S. (2002). Whole brain segmentation: Automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341–355.

Article  CAS  PubMed  Google Scholar 

Fischl, B., Salat, D. H., van der Kouwe, A. J., Makris, N., Segonne, F., Quinn, B. T., & Dale, A. M. (2004). Sequence-independent segmentation of magnetic resonance images. NeuroImage, 23 Suppl 1, S69-84. https://doi.org/10.1016/j.neuroimage.2004.07.016

Glasser, M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B., Andersson, J. L., Xu, J., Jbabdi, S., Webster, M., Polimeni, J. R., Van Essen, D. C., Jenkinson, M., & Consortium, W. U. M. H. (2013). The minimal preprocessing pipelines for the Human Connectome Project. NeuroImage, 80, 105–124. https://doi.org/10.1016/j.neuroimage.2013.04.127

Glasser, M. F., Smith, S. M., Marcus, D. S., Andersson, J. L., Auerbach, E. J., Behrens, T. E., Coalson, T. S., Harms, M. P., Jenkinson, M., & Moeller, S. (2016). The human connectome project’s neuroimaging approach. Nature Neuroscience, 19(9), 1175–1187.

Article  PubMed  PubMed Central  Google Scholar 

Glasser, M. F., Coalson, T. S., Bijsterbosch, J. D., Harrison, S. J., Harms, M. P., Anticevic, A., Van Essen, D. C., & Smith, S. M. (2018). Using Temporal ICA to selectively remove global noise while preserving global signal in functional MRI data. Neuroimage, 181, 692–717.

Article  PubMed  Google Scholar 

Gordon, E. M., Laumann, T. O., Gilmore, A. W., Newbold, D. J., Greene, D. J., Berg, J. J., Ortega, M., Hoyt-Drazen, C., Gratton, C., Sun, H., Hampton, J. M., Coalson, R. S., Nguyen, A. L., McDermott, K. B., Shimony, J. S., Snyder, A. Z., Schlaggar, B. L., Petersen, S. E., Nelson, S. M., & Dosenbach, N. U. F. (2017). Precision functional mapping of individual human brains. Neuron, 95(4), 791–807e797. https://doi.org/10.1016/j.neuron.2017.07.011

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grabner, G., Janke, A. L., Budge, M. M., Smith, D., Pruessner, J., & Collins, D. L. (2006). Symmetric atlasing and model based segmentation: an application to the hippocampus in older adults. Medical Image Computing and Computer-Assisted Intervention–MICCAI 2006: 9th International Conference, Copenhagen, Denmark, October 1–6, 2006. Proceedings, Part II 9.

Greve, D. N., & Fischl, B. (2009). Accurate and robust brain image alignment using boundary-based registration. [Evaluation Study] NeuroImage, 48(1), 63–72. https://doi.org/10.1016/j.neuroimage.2009.06.060

Article  PubMed  Google Scholar 

Jenkinson, M. (2018). BET User Guide. FMRIB ANalysis Group. Retrieved August 2 from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide

Jenkinson, M., Beckmann, C. F., Behrens, T. E., Woolrich, M. W., & Smith, S. M. (2012). FSL NeuroImage, 62(2), 782–790.

Article  PubMed  Google Scholar 

Karimpoor, M., Tam, F., Strother, S. C., Fischer, C. E., Schweizer, T. A., & Graham, S. J. (2015). A computerized tablet with visual feedback of hand position for functional magnetic resonance imaging. Frontiers in Human Neuroscience, 9, 150.

Article  PubMed  PubMed Central  Google Scholar 

Klein, A., Ghosh, S. S., Avants, B., Yeo, B. T., Fischl, B., Ardekani, B., Gee, J. C., Mann, J. J., & Parsey, R. V. (2010). Evaluation of volume-based and surface-based brain image registration methods. Neuroimage, 51(1), 214–220. https://doi.org/10.1016/j.neuroimage.2010.01.091

Article  PubMed  Google Scholar 

Michon, K. J., Khammash, D., Simmonite, M., Hamlin, A. M., & Polk, T. A. (2022). Person-specific and precision neuroimaging: Current methods and future directions. Neuroimage, 263, 119589. https://doi.org/10.1016/j.neuroimage.2022.119589

Article  PubMed  Google Scholar 

Mohapatra, S., Gosai, A., & Schlaug, G. (2023). Brain extraction comparing segment anything model (sam) and fsl brain extraction tool. arXiv preprint arXiv:2304.04738.

Mumford, J. A. (2017). FEAT registration workaround. Retrieved June 1 from https://mumfordbrainstats.tumblr.com/post/166054797696/feat-registration-workaround

Napadow, V., Dhond, R., Conti, G., Makris, N., Brown, E. N., & Barbieri, R. (2008). Brain correlates of autonomic modulation: Combining heart rate variability with fMRI. Neuroimage, 42(1), 169–177.

Article  PubMed  Google Scholar 

Nili, H., Wingfield, C., Walther, A., Su, L., Marslen-Wilson, W., & Kriegeskorte, N. (2014). A toolbox for representational similarity analysis. PLoS Computational Biology, 10(4), e1003553.

Novosad, P., Collins, D. L., & Neuroimaging, A. D., I (2018). An efficient and accurate method for robust inter-dataset brain extraction and comparisons with 9 other methods. Human Brain Mapping, 39(11), 4241–4257. https://doi.org/10.1002/hbm.24243

Article  PubMed  PubMed Central  Google Scholar 

Oldfield, R.C. (1971). The assessment and analysis of handedness: the Edinburgh inventory. Neuropsychologia, 9(1), 97–113. https://doi.org/10.1016/0028-3932(71)90067-4.

Philip, B. A., & Frey, S. H. (2014). Compensatory changes accompanying chronic forced use of the nondominant hand by unilateral amputees. The Journal of Neuroscience: the Official Journal of the Society for Neuroscience, 34(10), 3622–3631. https://doi.org/10.1523/JNEUROSCI.3770-13.2014

Article  CAS  PubMed  Google Scholar 

Philip, B. A., Li, F., Hawkins-Chernof, E., Swamidass, V., & Zwir, I. (2023). Motor assessment with the STEGA iPad app to measure handwriting in children. American Journal of Occupational Therapy, 77(3).

Polimeni, J. R., Renvall, V., Zaretskaya, N., & Fischl, B. (2018). Analysis strategies for high-resolution UHF-fMRI data. Neuroimage, 168, 296–320.

Article  PubMed  Google Scholar 

Quilis-Sancho, J., Fernandez-Blazquez, M. A., & Gomez-Ramirez, J. (2020). A comparative analysis of automated MRI brain segmentation in a large longitudinal dataset: Freesurfer vs. FSL. bioRxiv. https://doi.org/10.1101/2020.08.13.249474

Renvall, V., Witzel, T., Wald, L. L., & Polimeni, J. R. (2016). Automatic cortical surface reconstruction of high-resolution T1 echo planar imaging data. Neuroimage, 134, 338–354. https://doi.org/10.1016/j.neuroimage.2016.04.004

Article  PubMed  Google Scholar 

Seitzman, B. A., Gratton, C., Marek, S., Raut, R. V., Dosenbach, N. U. F., Schlaggar, B. L., Petersen, S. E., & Greene, D. J. (2020). A set of functionally-defined brain regions with improved representation of the subcortex and cerebellum. NeuroImage, 206, 116290. https://doi.org/10.1016/j.neuroimage.2019.116290

Siegel, J. S., Power, J. D., Dubis, J. W., Vogel, A. C., Church, J. A., Schlaggar, B. L., & Petersen, S. E. (2014). Statistical improvements in functional magnetic resonance imaging analyses produced by censoring high-motion data points. Human Brain Mapping, 35(5), 1981–1996. https://doi.org/10.1002/hbm.22307

Article  PubMed  Google Scholar 

Smith, S. M. (2002). Fast robust automated brain extraction. Human Brain Mapping, 17(3), 143–155.