When and where we meet: Monday and Wednesday 2:30-3:45pm , Rm 109 Stuit Hall
| Week | Date | Topic | Readings/Videos | Labs | |
|---|---|---|---|---|---|
| Unit 1: Introduction to MRI/fMRI methodology | |||||
| 1 | 01/17/18 | Introduction to the class: why use MRI and fMRI in cognitive neuroscience? Lecture slides |
Aguirre 2014 |
Start working on installing your virtual machine Lab 00 | |
| 2 | 01/22/18 | MRI Physics Lecture slides |
Noll Primer on MRI/fMRI Video |
| |
| 01/24/18 | fMRI BOLD contrast Lecture slides |
Logothetis 2001 |
| ||
| Unit 2: Preprocessing | |||||
| 3 | 01/29/18 | Technical landscape of MRI processing Lecture slides |
Handbook Ch 1 COBIDAS report: best practices |
||
| 01/31/18 | What are images | Handbook Ch 2 |
Software Intro Lab 01 | ||
| 4 | 02/05/18 | Preprocesing overview Lecture slides |
Handbook Ch 3 |
| |
| 02/07/18 | Image processing basics |
Image processing basics Lab 02 | |||
| 5 | 02/12/18 | Structural image quality Lecture slides |
mriqc Esteban et al. 2017 | ||
| 02/14/18 | Practice with spatial registration |
Handbook Ch 4 | Lab 03 | ||
| 6 | 02/19/18 | Registration wrap-up Lecture slides |
Spatial Transforms primer Registration primer Registration case studies primer | | |
| 02/21/18 | Registration of functional image and mapping masks between image spaces |
|
Lab 04 | ||
| 7 | 02/26/18 | fMRI preprocessing: Motion correction and slice-timing Lecture slides |
Handbook, p41-49 |
| |
| 02/28/18 | fMRI preprocessing: Detecting motion, motion correction, and slice-timing |
mriqc fsl motion outliers |
Lab 05 | ||
| 8 | 03/05/18 | fMRI preprocessing: ICA-denoising & temporal filtering Lecture slides |
Pruim et al, 2015 |
| |
| 03/07/18 | ICA-denoising & temporal filtering Lecture slides |
ICA-AROMA manual |
Lab 06 | ||
| Spring Break | |||||
| Unit 3: Statistical analyses | |||||
| 9 | 03/19/18 | Statistical analysis: single subject task analysis Lecture slides |
Handbook Ch 5 Video: matrix algebra primer Video: multiple regression with matrices |
| |
| 03/21/18 | Building a single subject task model |
Videos: first level models review Video: contrasts in linear models Mumford et al., 2015 |
Lab 07 | ||
| 10 | 03/26/18 | Task design considerations Lecture slides |
Amaro & Barker 2006 |
| |
| 03/28/18 | Building a task to run in the scanner |
Videos on estimating efficient designs optseq |
Lab 08 | ||
| 11 | 04/02/18 | Group analyses Lecture slides |
Handbook Ch 6 Handbook Appendix A GLM review Videos: Mixed models for imaging |
| |
| 04/04/18 | Building a between-subjects statistical model |
Example GLM designs Video: mean centering regressors |
Lab 09 | ||
| 12 | 04/09/18 | Statistical inference on images Lecture slides |
Handbook Ch 7 Eklund et al., 2016 Videos on thresholding methods |
| |
| 04/11/18 | Task analysis: putting it all together | Sarter, Bernston, Cacioppo, 1996 Kriegeskorte et al., 2009 |
Lab 10 | ||
| 13 | 04/16/18 | Introduction to diffusion imaging Lecture slides |
Jones 2008 Jones et al., 2013 TBSS primer |
| |
| 04/18/18 | Introduction to diffusion data |
Blog and supplementary video |
Lab 11 | ||
| 14 | 04/23/18 | Resting state functional connectivity Lecture slides |
Van Dijk et al., 2010 Murphy & Fox, 2017 |
| |
| 04/25/18 | Resting state functional connectivity |
|
Lab 12 | ||
| Unit 4: Reporting your results | |||||
| 15 | 04/30/18 | Final project working session |
Handbook Ch 10 COBIDAS report |
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| 05/02/18 | Final project working session |
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| 16 | 05/07/18 | Final project notebooks due |
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