University of Southern California

USC Neuroscience

Cognitive Neuroscience and Neuroimaging Methods

The Cognitive Neuroscience Journal Club and the Neuroimaging Methods Workshop have been combined this year to provide a forum for an ongoing conversation about recent topics in cognitive neuroscience and the methods used to implement this research. We hope to cover a wide range of topics (e.g., emotion, social cognition, consciousness, perception, attention, language, fMRI, TMS, EEG, psychopharmacology, genetics, multivariate stats, computational modeling), and hope to provide a forum where people from different disciplines can come together to engage in insightful discussions. This journal club is meant to be a resource. One of the main aims of this journal club will be to initiate interactions between the neuroimaging community members to help bridge gaps in methodological knowledge in neuroimaging research. To be specific, a main goal of the journal club is to have researchers who are experienced in structural and functional MRI analysis techniques to lead step-by-step tutorials on some of the various methods in these fields. Attendees should be able to walk away with an ample idea of how to implement the analyses on their own. Additionally, we hope to combine and make freely available notes, tutorials, demos, etc. on this website.

We will meet every Wednesday from 2-3pm in HNB small conference room (120F).

For more information, or to join the mailing list, please contact Mona Sobhani

Wednesday, June 1, 2011 -- Meghen Miles (VBM and BrainSuite), Glenn Fox (DTI), and Jonas Kaplan (MVPA)

-Program Downloads:
Trackvis and diffusion toolkit

FSL VBM instructions MM (PDF).

PyMVPA installation instructions for Macs here
- MVPA preprocessing in FSL mvpa_preprocess.txt.
PyMVPA demo:

Glenn's powerpoint:
Hagmann2006 DTI paper Hagmann_et_al._2006_RadioGraphics.PDF .

Jonas' Workshop Terminal Output Workshop_Terminal_Output.txt.

Thursday, June 16, 2011 -- Lei Liew (Statistical Analysis Programs, etc)
Lei's powerpoint Liew_Neuroimaging_Workshop_06_16_2011.pdf .
Lei's handout Liew_Useful_Links.doc.
Recording: Lei's talk
USC Scripts Database

Thursday, June 23, 2011 -- Fei Yang (psychophysiological recording in the scanner and its applications)
PhLem toolbox
Fei's powerpoint physiology_denoising_Fei.pdf.
Fei's demo script demosteps_script_Fei_2.txt.
Fei's sample data please email Mona for this file at Mona Sobhani

Thursday, June, 30, 2011 -- Mona Sobhani (Meta-Analysis in Neuroimaging)
GingerALE and Suite
Mona's powerpoint Sobhani_Metaanalysis_workshop.pdf

Thursday, July, 7, 2011 - Tong Sheng, Helder Filipe, Fei Yang (Functional Connectivity)
Tong's powerpoint Tong_20110706_FxnConn.pdf
Helder's powerpoint Helder_How_to_run_PPI_in_FSL.pdf
PPI in SPM ( link to SPM manual , Chapter 33)
PPI in FSL (see Helder's powerpoint for other useful links)

Fei's SPM PPI script (Fei_PPI_demosteps.txt)

Thursday, July 14, 2011 -- Ben Files (Introduction to EEG)
Ben's powerpoint (BenFiles_An_introduction_to_EEG.pdf)
example data

Thursday, July 21, 2011 -- Tong Sheng (Resting State fMRI data in SPM, using DPARSF)
Tong's powerpoint (Tong_2011-07-21_RestingStatefMRISPM.pdf)

Thursday, August 4, 2011 -- Katie Garrison (Laterality Index in Brain Imaging Research)
Katie's powerpoint Katie_LI.pdf
Notes from Katie's talk Katie_LI.doc
LI-toolbox (email Marko Wilke,, to obtain toolbox)

Thursday, August 11, 2011 -- Lei Liew (pre-processing of fMRI data)
Lei's powerpoint Lei_Preprocessing_08_11_2011.pdf
Notes on Lei's talk Notes_Lei.doc
Useful Preprocessing Links: FSL tutorial, UCLA NITP Summer Course
(See Monti, 7/12/2011, Preprocessing)

Wednesday, October 13, 2011 -- Nichole Lighthall (Uses, Misuses, and Perception of Neuroimaging)
Wardlaw et al. (2011). "Can It Read My Mind?" - What do the Public and Experts Think of the Current (Mis)Uses of Neuroimaging?. (Wardlaw2011.pdf)
APA's advice on "How to work with the media":
APA's checklist for media interviews: :

Wednesday, November 3, 2011 --David Clewett (ICA and Dual Regression)
WATCH: David's Lecture
David's powerpoint Clewett_Dual_Regression_Workshop_2011.pdf
David's dual regression cartoon Clewett_Dual_Regression_Guide.jpeg
Ref papers Zuo2010_Clewett.pdf, Allen2011_FN_RestingBaseline_Clewett.pdf
dual regression script

Wednesday, December 14, 2011 -- Marc Lebel (Sparse Sampling in MRI)
WATCH: Marc's Lecture
Marc's powerpoint MarcLebel_SparseSampling.pdf

Wednesday, February 1, 2012 -- Farhan Baluch (Steady State Visual Evoked Potentials (SSVEP))
Farhan's powerpoint Farharn_SSVEPIntro.pdf

Wednesday, April 11, 2012 -- Sook-Lei Liew & David Clewett (Arterial Spin Labeling)
Sook Lei Liew's Powerpoint

David Clewett's Powerpoint

Suggested Reading.pdf

Wednesday, April 18, 2012 -- Nichole Lighthall (Power Analyses for fMRI)
Nichole's Lighthall's Powerpoint

Suggested reading: Desmond & Glover, 2002; Mumford & Nichols, 2008

fMRI Power, g Power

Wednesday, June 13, 2012 -- Brad Gasser (Cognitive Neuroscience of Non-human Primates)
Brad Gasser's Powerpoint

Suggested Reading: Miller & Cohen, 2001

Wednesday, August 1, 2012 -- Syed Ashrafallah

Syed's Powerpoint

Click for BrainStorm Tutorials



Brainvoyager functional analysis guide Brainvoyager_func_GF.doc

USC Scripts Database