[4] In some of his early work Nieto-Castanon helped develop novel methods for region of interest (ROI) analyses of fMRI data,[5] with a focus on multivariate techniques and the use of subject-specific ROIs, where regions of interest are defined differently for each person based on common anatomical or functional landmarks.

[8] In collaboration with Boston University's Neural Prosthesis Laboratory, Nieto-Castanon helped build a Neuroprosthetic device for real-time speech synthesis.

[9] This system was designed to allow patients with locked-in syndrome to produce speech by decoding signals from a neurotrophic electrode implanted in the brain.

His software has been since widely adopted in the field[15][16][17][18][19] and it is now regularly used in functional connectivity studies, with over 900 citations during 2021 alone[20] Nieto-Castanon has given numerous courses and lectures worldwide[21][22][23][24][25] and his work has been cited in over 8000 refereed journal articles to date.

Programming in Matlab, Nieto-Castanon won in 2009 and in 2011 the Color Bridge and Vines MathWorks collaborative-programming competitions.