Abraham A, Pedregosa F, Eickenberg M, Gervais P, Mueller A, Kossaifi J, Gramfort A, Thirion B, Varoquaux G (2014) Machine learning for neuroimaging with scikit-learn. Front Neuroinform. https://doi.org/10.3389/fninf.2014.00014

Amico E, Goñi J (2018) The quest for identifiability in human functional connectomes. Sci Rep 8(1):8254. https://doi.org/10.1038/s41598-018-25089-1

Article  PubMed  PubMed Central  Google Scholar 

Andersson JLR, Skare S, Ashburner J (2003) How to correct susceptibility distortions in spin-echo echo-planar images: Application to diffusion tensor imaging. Neuroimage 20(2):870–888. https://doi.org/10.1016/S1053-8119(03)00336-7

Article  PubMed  Google Scholar 

Andersson JLR, Sotiropoulos SN (2016) An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. Neuroimage 125:1063–1078. https://doi.org/10.1016/j.neuroimage.2015.10.019

Article  PubMed  Google Scholar 

Avants BB, Epstein CL, Grossman M, Gee JC (2008) Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal 12(1):26–41. https://doi.org/10.1016/j.media.2007.06.004

Article  PubMed  Google Scholar 

Avants BB, Tustison N, Johnson H (2009) Advanced Normalization Tools (ANTS) 2(365):1–35

Google Scholar 

Behzadi Y, Restom K, Liau J, Liu TT (2007) A component based noise correction method (CompCor) for BOLD and perfusion based fMRI. Neuroimage 37(1):90–101. https://doi.org/10.1016/j.neuroimage.2007.04.042

Article  PubMed  Google Scholar 

Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc: Ser B (Methodol) 57(1):289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x

Article  Google Scholar 

Bernstein-Eliav M, Tavor I (2024) The prediction of brain activity from connectivity: advances and applications. Neuroscientist 30(3):367–377. https://doi.org/10.1177/10738584221130974

Article  PubMed  Google Scholar 

Bijsterbosch JD, Beckmann CF, Woolrich MW, Smith SM, Harrison SJ (2019). The relationship between spatial configuration and functional connectivity of brain regions revisited. eLife. https://doi.org/10.7554/eLife.44890

Chen J, Tam A, Kebets V, Orban C, Ooi LQR, Asplund CL, Marek S, Dosenbach NUF, Eickhoff SB, Bzdok D, Holmes AJ, Yeo BTT (2022) Shared and unique brain network features predict cognitive, personality, and mental health scores in the ABCD study. Nat Commun 13(1):2217. https://doi.org/10.1038/s41467-022-29766-8

Article  PubMed  PubMed Central  Google Scholar 

Chyzhyk D, Varoquaux G, Milham M, Thirion B (2022) How to remove or control confounds in predictive models, with applications to brain biomarkers. GigaScience 11:giac014. https://doi.org/10.1093/gigascience/giac014

Article  PubMed  PubMed Central  Google Scholar 

Cole MW, Ito T, Schultz D, Mill R, Chen R, Cocuzza C (2019) Task activations produce spurious but systematic inflation of task functional connectivity estimates. Neuroimage 189:1–18. https://doi.org/10.1016/j.neuroimage.2018.12.054

Article  PubMed  Google Scholar 

Cordero-Grande L, Christiaens D, Hutter J, Price AN, Hajnal JV (2019) Complex diffusion-weighted image estimation via matrix recovery under general noise models. Neuroimage 200:391–404. https://doi.org/10.1016/j.neuroimage.2019.06.039

Article  PubMed  Google Scholar 

Dadi K, Rahim M, Abraham A, Chyzhyk D, Milham M, Thirion B, Varoquaux G, Initiative ADN (2019) Benchmarking functional connectome-based predictive models for resting-state fMRI. Neuroimage 192:115–134. https://doi.org/10.1016/j.neuroimage.2019.02.062

Article  PubMed  Google Scholar 

Dadi K, Varoquaux G, Machlouzarides-Shalit A, Gorgolewski KJ, Wassermann D, Thirion B, Mensch A (2020) Fine-grain atlases of functional modes for fMRI analysis. Neuroimage 221:117126. https://doi.org/10.1016/j.neuroimage.2020.117126

Article  PubMed  Google Scholar 

Demirtaş M, Ponce-Alvarez A, Gilson M, Hagmann P, Mantini D, Betti V, Romani GL, Friston K, Corbetta M, Deco G (2019) Distinct modes of functional connectivity induced by movie-watching. Neuroimage 184:335–348. https://doi.org/10.1016/j.neuroimage.2018.09.042

Article  PubMed  Google Scholar 

Deslauriers-Gauthier S, Zucchelli M, Frigo M, Deriche R (2020) A unified framework for multimodal structure-function mapping based on eigenmodes. Med Image Anal 66:101799. https://doi.org/10.1016/j.media.2020.101799

Article  PubMed  Google Scholar 

Dhollander T, Mito R, Raffelt D, Connelly A (2019). Improved white matter response function estimation for 3-tissue constrained spherical deconvolution

Dohmatob E, Richard H, Pinho AL, Thirion B (2021) Brain topography beyond parcellations: local gradients of functional maps. Neuroimage 229:117706. https://doi.org/10.1016/j.neuroimage.2020.117706

Article  PubMed  Google Scholar 

Finn ES (2021) Is it time to put rest to rest? Trends Cogn Sci 25(12):1021–1032. https://doi.org/10.1016/j.tics.2021.09.005

Article  PubMed  PubMed Central  Google Scholar 

Finn ES, Scheinost D, Finn DM, Shen X, Papademetris X, Constable RT (2017) Can brain state be manipulated to emphasize individual differences in functional connectivity? Neuroimage 160:140–151. https://doi.org/10.1016/j.neuroimage.2017.03.064

Article  PubMed  Google Scholar 

Finn ES, Shen X, Scheinost D, Rosenberg MD, Huang J, Chun MM, Papademetris X, Constable RT (2015) Functional connectome fingerprinting: Identifying individuals using patterns of brain connectivity. Nat Neurosci 18(11):1664–1671. https://doi.org/10.1038/nn.4135

Article  PubMed  PubMed Central  Google Scholar 

Friedman J, Hastie T, Tibshirani R (2008) Sparse inverse covariance estimation with the graphical lasso. Biostatistics 9(3):432–441. https://doi.org/10.1093/biostatistics/kxm045

Article  PubMed  Google Scholar 

Friston KJ, Frith CD, Frackowiak RSJ, Turner R (1995) v. Neuroimage 2(2, Part A):166–172. https://doi.org/10.1006/nimg.1995.1019

Article  PubMed  Google Scholar 

Glasser MF, Coalson TS, Robinson EC, Hacker CD, Harwell J, Yacoub E, Ugurbil K, Andersson J, Beckmann CF, Jenkinson M, Smith SM, Van Essen DC (2016) A multi-modal parcellation of human cerebral cortex. Nature 536(7615):171–178. https://doi.org/10.1038/nature18933

Article  PubMed  PubMed Central  Google Scholar 

Hannum A, Lopez MA, Blanco SA, Betzel RF (2023) High-accuracy machine learning techniques for functional connectome fingerprinting and cognitive state decoding. Hum Brain Mapp 44(16):5294–5308. https://doi.org/10.1002/hbm.26423

Article  PubMed  PubMed Central  Google Scholar 

Harris CR, Millman KJ, van der Walt SJ, Gommers R, Virtanen P, Cournapeau D, Wieser E, Taylor J, Berg S, Smith NJ, Kern R, Picus M, Hoyer S, van Kerkwijk MH, Brett M, Haldane A, del Río JF, Wiebe M, Peterson, P. et al. (2020) Array programming with NumPy. Nature 585(7825):357–362. https://doi.org/10.1038/s41586-020-2649-2

Haxby JV, Guntupalli JS, Connolly AC, Halchenko YO, Conroy BR, Gobbini MI, Hanke M, Ramadge PJ (2011) A common, high-dimensional model of the representational space in human ventral temporal cortex. Neuron 72(2):404–416. https://doi.org/10.1016/j.neuron.2011.08.026

Article  PubMed  PubMed Central  Google Scholar 

Hermundstad AM, Bassett DS, Brown KS, Aminoff EM, Clewett D, Freeman S, Frithsen A, Johnson A, Tipper CM, Miller MB, Grafton ST, Carlson JM (2013) Structural foundations of resting-state and task-based functional connectivity in the human brain. Proc Natl Acad Sci 110(15):6169–6174. https://doi.org/10.1073/pnas.1219562110

Article  PubMed  PubMed Central  Google Scholar 

Honey CJ, Sporns O, Cammoun L, Gigandet X, Thiran JP, Meuli R, Hagmann P (2009) Predicting human resting-state functional connectivity from structural connectivity. Proc Natl Acad Sci 106(6):2035–2040. https://doi.org/10.1073/pnas.0811168106

Article  PubMed  PubMed Central  Google Scholar 

Honey CJ, Thivierge J-P, Sporns O (2010) Can structure predict function in the human brain? Neuroimage 52(3):766–776. https://doi.org/10.1016/j.neuroimage.2010.01.071

Article  PubMed  Google Scholar 

Hunter JD (2007) Matplotlib: a 2D graphics environment. Comput Sci Eng 9(3):90–95. https://doi.org/10.1109/MCSE.2007.55

Article  Google Scholar 

Jalbrzikowski M, Liu F, Foran W, Klei L, Calabro FJ, Roeder K, Devlin B, Luna B (2020) Functional connectome fingerprinting accuracy in youths and adults is similar when examined on the same day and 1.5-years apart. Hum Brain Mapp 41(15):4187–4199. https://doi.org/10.1002/hbm.25118

Article  PubMed