Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses
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Abstract
Background
The choice of preprocessing pipeline introduces variability in neuroimaging analyses that affects the reproducibility of scientific findings. Features derived from structural and functional MRI data are sensitive to the algorithmic or parametric differences of preprocessing tasks, such as image normalization, registration, and segmentation to name a few. Therefore it is critical to understand and potentially mitigate the cumulative biases of pipelines in order to distinguish biological effects from methodological variance.
Methods
Here we use an open structural MRI dataset (ABIDE), supplemented with the Human Connectome Project, to highlight the impact of pipeline selection on cortical thickness measures. Specifically, we investigate the effect of (i) software tool (e.g., ANTS, CIVET, FreeSurfer), (ii) cortical parcellation (Desikan-Killiany-Tourville, Destrieux, Glasser), and (iii) quality control procedure (manual, automatic). We divide our statistical analyses by (i) method type, i.e., task-free (unsupervised) versus task-driven (supervised); and (ii) inference objective, i.e., neurobiological group differences versus individual prediction.
Results
Results show that software, parcellation, and quality control significantly affect task-driven neurobiological inference. Additionally, software selection strongly affects neurobiological (i.e. group) and individual task-free analyses, and quality control alters the performance for the individual-centric prediction tasks.
Conclusions
This comparative performance evaluation partially explains the source of inconsistencies in neuroimaging findings. Furthermore, it underscores the need for more rigorous scientific workflows and accessible informatics resources to replicate and compare preprocessing pipelines to address the compounding problem of reproducibility in the age of large-scale, data-driven computational neuroscience.
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Now published in GigaScience doi: 10.1093/gigascience/giaa155
Nikhil Bhagwat 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: nikhil153@gmail.com jean-baptiste.poline@mcgill.caAmadou Barry 2Lady Davis Institute for Medical Research, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteErin W. Dickie 3Kimel Family Translational Imaging-Genetics Research Lab, CAMH, Toronto, ON, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShawn T. Brown 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind …
Now published in GigaScience doi: 10.1093/gigascience/giaa155
Nikhil Bhagwat 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: nikhil153@gmail.com jean-baptiste.poline@mcgill.caAmadou Barry 2Lady Davis Institute for Medical Research, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteErin W. Dickie 3Kimel Family Translational Imaging-Genetics Research Lab, CAMH, Toronto, ON, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShawn T. Brown 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGabriel A. Devenyi 4Computational Brain Anatomy Laboratory, Douglas Mental Health Institute, Verdun, QC, Canada5Department of Psychiatry, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKoji Hatano 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth DuPre 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlain Dagher 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM. Mallar Chakravarty 4Computational Brain Anatomy Laboratory, Douglas Mental Health Institute, Verdun, QC, Canada5Department of Psychiatry, McGill University, Montreal, QC, Canada10Department of Biomedical Engineering, McGill UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCelia M. T. Greenwood 2Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada8Ludmer Centre for Neuroinformatics Mental Health, McGill University, Montreal, QC, Canada9Gerald Bronfman Department of Oncology; Department of Epidemiology, Biostatistics Occupational Health; Department of Human Genetics, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBratislav Misic 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid N. Kennedy 7Child and Adolescent Neurodevelopment Initiative, University of Massachusetts, Worcester, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJean-Baptiste Poline 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, Canada6Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada8Ludmer Centre for Neuroinformatics Mental Health, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: nikhil153@gmail.com jean-baptiste.poline@mcgill.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa155 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102614 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102615
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