Neuroimaging data analysis (GBIO0034)

13 Nov 2024, 14:00 → 18 Dec 2024, 18:00 Europe/Brussels

B-30/0-000 - Big meeting room (CRC)

Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)

This Indico event describes the content and planning for the course "Neuroimaging data analysis" (GBIO0034), formerly known as "Introduction to medical statistics" (STAT0722). The program is very similar but might be slightly updated from one year to the next, especially the later classes...

The course content is focused on the SPM software and its application to analyse neuroimaging data. The course will be illustrated with some example of data processing using the demo data from SPM. The material from last year's is still available; moreover the course in 2020 was taught online and the video recording are an excellent source of information. Not to be missed either, the slides and videos from past official SPM courses in London are all accessible online!

Class room & timetable

Six classes are planned, on Wednesdays from 14h till 17h with a mid-break. Those will take place in the "large meeting" room, aka. "Fluor" at the Cyclotron Research Centre, B30, on November 13, 20 & 27 and December 4, 11 & 18, as described here under. The exact program might be slightly adjusted.

Evaluation

This will consist in

• the oral presentation (~20min) of a peer-reviewed article in the field of neuroimaging.
• the focus should be on the methodological aspects and data processing overall.

Students are free to choose an article they find interesting but it should still be approved by C. Phillips.

Potential journals:

• Neuroimage, 
• Human Brain Mapping, 
• Frontiers in Brain Imaging Methods, 
• Imaging Neuroscience, 
• Aperture Neuro,
• ...

Potential papers, LIST TO BE UPDATED FOR 2024 !

• Eklund et al. Cluster Failure: Why fMRI Inferences for Spatial Extent Have Inflated False-Positive Rates. PNAS 2016. http://www.ncbi.nlm.nih.gov/pubmed/27357684

• Eklund et al. Cluster Failure Revisited: Impact of First Level Design and Physiological Noise on Cluster False Positive Rates. HBM 2019, https://doi.org/10.1073/pnas.1602413113

• Esteban et al. MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites. PLOS ONE 2017, https://doi.org/10.1371/journal.pone.0184661

• Esteban et al. FMRIPrep: a robust preprocessing pipeline for functional MRI. Nature Methods 2019, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6319393/

• Gyger et al. Temporal trajectory of brain tissue property changes induced by electroconvulsive therapy. NeuroImage 2021, https://doi.org/10.1016/j.neuroimage.2021.117895

• Huber et al. Evaluating the capabilities and challenges of layer-fMRI VASO at 3T. Aperture Neuro 2023, https://doi.org/10.52294/001c.85117

• Mortamet et al. Automatic quality assessment in structural brain magnetic resonance imaging. Magnetic Resonance in Medicine 2009, https://doi.org/10.1002/mrm.21992

• Pernet. Misconceptions in the use of the General Linear Model applied to functional MRI: a tutorial for junior neuro-imagers, Frontiers in Neuroscience 2014, https://www.frontiersin.org/articles/10.3389/fnins.2014.00001

• Reuter et al. Head motion during MRI acquisition reduces gray matter volume and thickness estimates. NeuroImage 2015, https://doi.org/10.1016/j.neuroimage.2014.12.006

• Smith & Nichols. Statistical Challenges in “Big Data” Human Neuroimaging. Neuron 2018, https://doi.org/10.1016/j.neuron.2017.12.018

Date, time & place:

• TBD (depending on the number of students, multiple dates could be planned)
• at the  CRC (B30), large meeting room

Wednesday, 13 November

14:00 → 17:00 Introduction to SPM + Spatial pre-processing, within subject & warping

Grande salle de réunion, B30 (CRC).

Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)

Wednesday, 20 November

14:00 → 17:00 Spatial pre-processing, unified segmentation & smoothing

Grande salle de réunion, B30 (CRC).

Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)

Wednesday, 27 November

14:00 → 17:00 GLM, contrast & statistical inference

Grande salle de réunion, B30 (CRC).

Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)

Wednesday, 4 December

14:00 → 17:00 Multiple comparison problem & solutions

Grande salle de réunion, B30 (CRC).

Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)

Wednesday, 11 December

14:00 → 17:00 Evoked-response fMRI design + Experimental design

Grande salle de réunion, B30 (CRC).

Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)

Wednesday, 18 December

14:00 → 17:00 Random Effect Analysis + Voxel base morphometry & Wrap up

Grande salle de réunion, B30 (CRC).

Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)