saidejp/Curso_Neuroimagen_Reproducibilidad

Repositorio con material de la exposición "Uso de bases de datos libres y reproducibilidad" como parte del curso "Introducción a la neuroimagen computacional para investigación en psiquiatría" impartido en el Instituto Nacional de Psiquiatría “Ramón de la fuente Muñiz” del 11 al 13 de diciembre del 2017, coordinado por el Dr. Eduardo Garza Villarreal.

Sobre Reproducibilidad

Lecturas importantes

• Why Most Published Research Findings Are False: http://robotics.cs.tamu.edu/RSS2015NegativeResults/pmed.0020124.pdf
• 1,500 scientists lift the lid on reproducibility: https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970
• Power failure: why small sample size undermines the reliability of neuroscience: https://www.nature.com/articles/nrn3475
• A manifiesto for reproducible science: https://www.nature.com/articles/s41562-016-0021.pdf
• Scanning the Horizon: Towards transparent and reproducible neuroimaging research: https://www.biorxiv.org/content/biorxiv/early/2016/10/25/059188.full.pdf
• Best Practices in Data Analysis and Sharing in Neuroimaging using MRI: https://www.biorxiv.org/content/biorxiv/early/2016/05/20/054262.full.pdf

Sitios de interés

• Center for reproducible neuroscience: http://reproducibility.stanford.edu
• Human Connectome Project: https://www.humanconnectome.org

Herramientas

• p-hacker: http://shinyapps.org/apps/p-hacker/
• NeuroPowerTools: http://neuropowertools.org
• BIDS: http://bids.neuroimaging.io
• Neurosynth: http://neurosynth.org
• Nipype: http://nipype.readthedocs.io/en/latest/
• Jupyter: http://jupyter.org
• Docker: https://www.docker.com
• Github: https://github.com/topics/neuroscience
• Open Science Framework: https://osf.io
• ClinicalTrials: https://clinicaltrials.gov

Bases de datos libres

• OASIS: http://www.oasis-brains.org
• Child Mind Institute: http://fcon_1000.projects.nitrc.org
• NKI: http://fcon_1000.projects.nitrc.org/indi/pro/nki.html
• ABIDE: http://fcon_1000.projects.nitrc.org/indi/abide/
• Neurovault: https://neurovault.org
• OpenfMRI: https://openfmri.org
• Un ejemplo de HCP: https://www.humanconnectome.org/study/hcp-young-adult/data-releases
• ADNI: http://adni.loni.usc.edu

Sobre fMRI

Principales programas para análisis de MRI

• FSL:https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
• SPM: http://www.fil.ion.ucl.ac.uk/spm/
• CONN: https://www.nitrc.org/projects/conn
• AFNI: https://afni.nimh.nih.gov

Programación

• Bash:

  • https://www.datacamp.com/courses/introduction-to-shell-for-data-science
  • https://www.codecademy.com/learn/learn-the-command-line

• MATLAB:

  • https://www.coursera.org/learn/matlab

• Python:

  • https://www.datacamp.com/courses/intro-to-python-for-data-science

• R:

  • https://www.datacamp.com/courses/free-introduction-to-r

Recursos:

• Python y Neuroimagen: http://nipy.org
• R y Neuroimagen: https://neuroconductor.org
• Python y paradigmas experimentales: http://www.psychopy.org
• Máquina virtual con todo lo esencial para fMRI: http://neuro.debian.net

¿Cómo puedo seguir aprendiendo acerca de neuroimagen?

• IMAIOS: https://www.imaios.com/en/e-Courses/e-MRI

• Neuroimaging Tutorials: https://talks.stanford.edu/tutorials/neuroimaging-tutorials/

• Nipy: http://nipy.org/nipy/users/tutorial.html

• Neuroimaging Analysis within R: http://johnmuschelli.com/imaging_in_r/

• Introduction to Neurohacking In R: https://www.coursera.org/learn/neurohacking

• Dos excelentes cursos en línea (gratuitos), enfocado en las bases y los avances recientes en el campo de fMRI (principalmente conceptual):

  • Principles of fMRI 1: https://www.coursera.org/learn/functional-mri
  • Principles of fMRI 2: https://www.coursera.org/learn/functional-mri-2

• Blog con tutoriales de fMRI: http://andysbrainblog.blogspot.mx; http://www.fmri4newbies.com/tutorials/

• Resources for data driven neuroscientists: https://pbeukema.github.io/LabHacks/

Libros

• Functional Magnetic Resonance Imaging: http://sites.sinauer.com/fmri3e/
• Handbook of Functional MRI Data Analysis: http://www.fmri-data-analysis.org
• Handbook of Neuroimaging Data Analysis: https://www.crcpress.com/Handbook-of-Neuroimaging-Data-Analysis/Ombao-Lindquist-Thompson-Aston/p/book/9781482220971

Artículos

• The Statistical Analysis of fMRI Data. http://www.stat.columbia.edu/~martin/Papers/STS282.pdf
• Nature focus on human brain mapping: http://www.nature.com/neuro/focus/humanbrainmapping/index.html

Neuroimagen y psiquiatría

• The Challenges and Promise of Neuroimaging in Psychiatry http://www.cell.com/neuron/pdf/S0896-6273(11)01095-6.pdf

• Computational psychiatry as a bridge from neuroscience to clinical applications. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443409/pdf/nihms869778.pdf

• Neuroimaging in psychiatry: bringing neuroscience into clinical practice. http://bjp.rcpsych.org/content/bjprcpsych/201/1/1.full.pdf

• Neuroimaging in psychiatry: from bench to bedside. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807751/pdf/fnhum-03-049.pdf

Contacto:

Dr. Eduardo Garza-Villarreal: egarza@gmail.com; Josué Mendoza: rjmdzar@gmail.com