I turn my problems into programs. Neuroscience PhD. MRI pipelines, longitudinal data, reproducible science.
15+ years extracting signal from complex biomedical and neuroimaging datasets — as principal neuroimaging analyst on three NIH-funded longitudinal cohorts, postdoctoral fellow in neurotrauma, and now as a neurotechnology adviser and AI domain expert. I build the infrastructure that makes analyses reproducible, not just the analyses.
11 peer-reviewed publications · 397 citations · h-index: 10
Multimodal MRI Analysis → fMRI · DTI · MRS · Volumetric
Pipeline Development → Containerized · HPC · BIDS-compliant
Longitudinal Modeling → Mixed-effects · MLM · Brain-behavior
AI & Neurotechnology → Model evaluation · Neurofeedback · Protocol design
Organized by where each tool sits in a neuroimaging workflow — acquisition through analysis.
Data Acquisition & Conversion
| Project | Description | Stack |
|---|---|---|
| BIDS_convert | DICOM-to-BIDS converter across all major modalities with parallel processing and provenance archival | Shell |
Processing Pipelines
| Project | Description | Stack |
|---|---|---|
| dwiforge | ML-enhanced DTI processing pipeline with checkpointing, structured logging, and automated QC — methods paper in preparation | Shell · Python |
Extraction & Tabulation
| Project | Description | Stack |
|---|---|---|
| fsglean | BIDS-aware extraction of FreeSurfer stats into tidy, longitudinal tables | Python |
| QSI-extract | BIDS-aware extraction of NODDI and DTI scalars from QSIPrep/QSIRecon into tidy longitudinal tables, with NODDI assumption auditing and QC propagation | Python |
Statistical Analysis
| Project | Description | Stack |
|---|---|---|
| neuromediate | Mediation analysis framework for MRI data | Python |
| data-trance | Config-driven pipeline that diagnoses a column's distribution (skew, kurtosis, normality) before touching it, then recommends and applies the least-lossy appropriate transform — rule-based, ML, or DL recommender methods | Python |
Novel Methods & Simulation
| Project | Status | Description | Stack |
|---|---|---|---|
| SMILD | 🚧 Active — POC validated; production two-branch solver (RotInv/LEMONADE) and ABCD Study validation in progress | Novel voxelwise reliability measure for the Standard Model diffusion-MRI degeneracy — quantifies whether biophysical microstructure estimates (NODDI, SMT, WMTI) are actually identifiable from the data. Theory paper in docs/ |
Python |
| krige-bold | 🧪 Pilot — synthetic-data validated (incl. ablation vs. rank-truncation alone); not yet benchmarked on real fMRI or against MPPCA/NORDIC | Geostatistical Functional Denoising for fMRI BOLD time series — combines Marchenko–Pastur random-matrix theory (objective signal/noise rank selection) with per-component functional kriging (spatially-varying smoothing) in place of one fixed isotropic kernel | Python |
| NERVES | ✅ Verified — core NDE math independently checked 3 ways; 2 real bugs found & fixed (report-writing crash, FA mislabeling); CI added | Normalized Entropy Representation of Voxelwise Eigenvalue Spectra for microstructural diffusion mapping | Python |
| kinetispect | 🚧 Active | fMRS simulator for functional magnetic resonance spectroscopy | — |
Infrastructure & Utilities
| Project | Description | Stack |
|---|---|---|
| NeuroRig | Assess your system's ability to run common MRI processing software | Python |
| maintainctl | System-wide update & cache-cleanup CLI (merged successor to updoot-inator + del-doot-inator) | Shell |
Other Research Tooling
| Project | Description | Stack |
|---|---|---|
| surveykit-ml | Statistical analysis and machine learning toolkit for survey data — factor analysis, reliability testing, group comparisons, and classification/clustering for reproducible research pipelines | Python |
Outside the neuroimaging stack — writing, tooling, and career-adjacent projects.
| Project | Description | Stack |
|---|---|---|
| Comprehensive-Stats-Book | In-depth statistics reference document | — |
| gistcv | Uses your resume/CV to generate job search terms | JavaScript |
| NeuroVersatilist | Website | HTML |
Beckwith TJ, Dietrich KN, Wright JP, Altaye M, Cecil KM. (2021). Criminal arrests associated with reduced regional brain volumes in an adult population with documented childhood lead exposure. Environmental Research, 201: 111559.
Beckwith T, Cecil K, Altaye M, et al. (2020). Reduced gray matter volume and cortical thickness associated with traffic-related air pollution in a longitudinally studied pediatric cohort. PLOS ONE, 15(1): e0228092.
Beckwith TJ, Dietrich KN, Wright JP, Altaye M, Cecil KM. (2018). Reduced regional volumes associated with total psychopathy scores in an adult population with childhood lead exposure. Neurotoxicology, 67: 1–26.
Neuroimaging: FSL · AFNI · FreeSurfer · fMRIPrep · SPM · MRtrix3 · ANTs · dipy
Programming: Python · R · MATLAB · Bash · SQL
Infrastructure: Docker · Singularity · HPC/SLURM · BIDS · Git
Statistics: Mixed-effects models · GLM · Mediation · Multivariate methods · Longitudinal trajectory analysis
Languages: English (native) · Spanish (basic)
- 🧬 Neurotechnology Adviser @ MetaBrain Labs — Pilot study design and neuroscience integration for an AI-powered cognitive performance platform
- 🤖 Subject Matter Expert (Oracle) @ Outlier — Neuroscience and biomedical AI model training and evaluation
- 🔭 Building open-source neuroimaging infrastructure
Open to research scientist and imaging scientist roles at the intersection of rigorous science and real decisions.
