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"Why & How" Seminar Series

Lectures are held about twice per month on Thursday at 6PM, in the 2204 conference room of Building 149. Snacks are served 20 minutes prior to the talk (no food is allowed inside the conference room).

The Why-N-How seminar meets (almost) every second week for a presentation by MGH Martinos Center experts on a wide range of topics relevant to our work at the center. The talks are particularly geared toward research assistants, grad students, post-docs, and clinical fellows, but they are open to everyone. This year there will be a big emphasis on software tools, especially those used for neuroimaging analysis. We will also have talks overviewing most of the major imaging modalities used at the center (MRI, PET, EEG, MEG, optical, TMS, and others). We have some outstanding speakers lined up, so stay tuned as our schedule takes shape! You will find the schedule below as well as slides from past talks.


Organizers: Clarissa Cooley (clarissa@nmr.mgh.harvard.edu) and Shahin Nasr (shahin@nmr.mgh.harvard.edu)
Mailing List: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/whynhow


In order to better respond to your interests, let us know what you would like to learn more about! Below are the schedules from past years, which will serve as the basis for this year's talks. If you'd like us to add a topic, send us an email at clarissa@nmr.mgh.harvard.edu and/or shahin@nmr.mgh.harvard.edu and we'll try to make it happen.


In 2016, we started recording Why-N-How talks. Look for them to appear on the Martinos Center YouTube channel.


Past organizers include: Jason Stockmann, Laura Lewis, Hamdi Eryilmaz, Anna Rieckmann, and Khaldoun Makhoul.

Overview of functional MRI presented in 2016 by Natalia Zaretskaya.
Overview of functional MRI physics and data processing presented in 2016 by Dr. Natalia Zaretskaya.




Calendar 2017-18:

Date Time Location Speaker Topic References Lecture Slides
September 14, 2017 6:00 pm CNY149-2204 Sam Mehl and Thomas Witzel Intro to Computing at the Martinos Center
September 21, 2017 6:00 pm CNY149-2204 Iman Aganj Introduction to Launchpad Tool for batch processing
October 5, 2017 6:00 pm CNY149-2204 Patrick McDaniel Introduction to MR Physics [1]
October 19, 2017 6:00 pm CNY149-2204 Eric Gale Introduction to MRI Contrast Agents
November 2, 2017 6:00 pm CNY149-2204 Marco Loggia Intro to Neuroanatomy MOVIE
November 16, 2017 6:00 pm CNY149-2204 Sam Mehl Overview of Remote Computing Tools at Martinos [2]
November 30, 2017 6:00 pm CNY149-2204 Emma Boyd Introduction to FreeSurfer analysis software [3]
December 14, 2017 6:00 pm CNY149-2204 Jason Stockmann Introduction to MRI Artifacts [4]
January 18, 2018 6:00 pm CNY149-2204 Angel Torrado Carvajal and Markus Schirmer Introduction to Parallel Processing and Machine Learning [5] [6]
January 25, 2018 6:00 pm CNY149-2204 Melissa Haskell Introduction to MATLAB [7]
February 1, 2018 5:30 pm CNY114- Conf. Room D1 Mathworks Team Demystifying deep learning: A practical approach in MATLAB
February 8, 2018 5:30 pm CNY114- Conf. Room D1 Mathworks Team Parallel and Distributed Computing with MATLAB
February 15, 2018 6:00 pm CNY149-2204 Isik Karahanoglu Introduction to Functional MRI Data Analysis Using FSFast
February 22, 2018 6:00 pm CNY149-2204 Anastasia Yendiki Introduction to Diffusion-Weighted MRI
March 1, 2018 6:00 pm CNY149-2204 Koene Van Dijk Introduction to Functional Connectivity Analysis
March 8, 2018 6:00 pm CNY149-2204 Sheraz Khan Master EEG/MEG in 1 Hour
March 22, 2018 6:00 pm CNY149-2204 Laura Lewis Introduction to EEG/fMRI: Neuroimaging with High Spatial and Temporal Resolution
April 5, 2018 6:00 pm CNY149-2204 Eva Ratai Introduction to Spectroscopy
April 19, 2018 6:00 pm CNY149-2204 Christin Sander Introduction to Positron Emission Tomography
May 3, 2018 6:00 pm CNY149-2204 TBD TBD
May 17, 2018 6:00 pm CNY149-2204 Abbas Yaseen and Stefan Carp Introductory Biomedical Optics
May 31, 2018 6:00 pm CNY149-2204 Kwangyeol Baek Introduction to Electrophysiology for Neuroimaging Scientists





Calendar 2016-17:

Date Time Location Speaker Topic References Lecture Slides
September 8, 2016 6:00 pm CNY149-2204 Lee Tirrell, Thomas Witzel, Ryan Feeley Intro to Computing at the Martinos Center (including Launchpad) [8], [9]
September 22, 2016 6:00 pm CNY149-2204 Jason Stockmann Intro to MR Physics
October 6, 2016 6:00 pm CNY149-2204 Emma Boyd Introduction to FreeSurfer analysis software [10]
October 20, 2016 6:00 pm CNY149-2204 Aapo Nummenmaa Introduction to Matlab
November 3, 2016 6:00 pm CNY149-2204 Sam Zorowitz Introduction to Python [11]
November 17, 2016 6pm CNY149-2204 Sam Mehl Remote Computing [12]
December 1, 2016 6:00 pm CNY149-2204 Cancelled Cancelled
February 2, 2017 6:00 pm CNY149-2204 Marco Loggia Introduction to Neuroanatomy [13]
March 2, 2017 6:00 pm CNY149-2204 Anastasia Yendiki Intro. to Diffusion-Weighted MRI [14]
March 16, 2017 6:00 pm CNY149-2204 Sheraz Khan Master EEG/MEG in 1 hour
March 30, 2017 6:00 pm CNY149-2204 Anna Blazejewska Introduction to data processing with FSL [15]
April 13, 2017 6:00 pm CNY149-2204 Mahanand Belathur Suresh Technical Writing with LaTeX [16]
May 18, 2017 6:00 pm CNY149-2204 Christin Sander Intro to Positron Emission Tomography
May 25, 2017 6:00 pm CNY149-2204 Lauri Tuominen Studying neurotransmitter systems with PET [17]
June 22, 2017 6:00 pm CNY149-2204 Shahin Nasr High-resolution fMRI





Calendar 2015-16:

Date Time Location Speaker Topic References Lecture Slides
September 10, 2015 6pm CNY149-2204 Sam Mehl and Jon Kaiser Intro to Computing at the Martinos Center [18] 
 [19]
September 24, 2015 6pm CNY149-2204 Jason Stockmann Intro to Magnetic Resonance Physics and basic principles of imaging
October 8, 2015 6pm CNY149-2204 Natalia Zaretskaya Intro to SPM and FsFAST analysis tools [20]
October 22, 2015 (Note different time and place!) 4:30-6:30 pm CNY75 Conference room Alyssa Silverman and Brandon Armstrong from MathWorks Special MathWorks seminar highlighting image analysis tools and machine learning
October 8, 2015 6pm CNY149-2204 Natalia Zaretskaya Intro to SPM and FsFAST analysis tools [21]
October 22, 2015 (Note different time and place!) 4:30-6:30 pm CNY75 Conference room Alyssa Silverman and Brandon Armstrong from MathWorks Special MathWorks seminar highlighting image analysis tools and machine learning
October 22, 2015 4:30-6pm Building 75 Conference Room Alyssa Silverman Special presentation by Mathworks engineers
November 19, 2015 6pm CNY149-2204 Hari Bharadwaj Statistics
December: Tues. the 1st and Wed. the 2nd, 2015, *NOTE CHANGE OF DAY* 6pm !!! BAY 2 !!! Dylan Tisdall MRI scanner demonstration
January 21, 2016 6 pm CNY149-2204 Sheraz Khan Master MEG/EEG in one hour
February 4, 2016 6 pm CNY149-2204 Laura Lewis Intro to EEG/fMRI: Neuroimaging with high spatial and temporal resolution [22]
February 18, 2016 6 pm CNY149-2204 Marco Loggia Intro to Neuroanatomy
March 17, 2016 6pm CNY149-2204 Christin Sander Intro to Positron Emission Tomography (PET) and PET/MRI
March 31, 2016 6pm CNY149-2204 Koene van Dijk Functional connectivity MRI: The basics and scanning at 7 Tesla
April 14, 2016 6pm CNY149-2204 Eva Ratai Introduction to Magnetic Resonance Spectroscopy: Principles and Clinical Applications [23]







Calendar 2014-15:

Date Time Location Speaker Topic References Lecture Slides
September 18, 2014 6pm CNY149-2204 Sam Mehl and Jon Kaiser Intro to Computing at the Martinos Center [24] [25]
October 2, 2014 6pm CNY149-2204 Allison Stevens Intro to Freesurfer [26]
October 16, 2014 6pm CNY149-2204 Aapo Nummenmaa Intro to Matlab [27]
October 30, 2014 6pm CNY149-2204 Martin Luessi Intro to Python
November 13, 2014 6pm CNY149-2204 Jason Stockmann Intro to MRI physics
December 10 & 11, 2014 6pm !!! BAY 2 !!! Dylan Tisdall MRI scanner demonstration
January 29, 2015 6pm CNY149-2204 Hari Bharadwaj Statistics [28]
February 12, 2015 6pm CNY149-2204 Sheraz Khan Master MEG/EEG in one hour
February 26, 2015 6pm CNY149-2204 Anastasia Yendiki Diffusion-weighted MRI [29]
March 12, 2015 6pm CNY149-2204 Marco Loggia Intro to neuroanatomy [30]
March 26, 2015 6pm CNY149-2204 Natalia Zaretskaya Intro to functional MRI and FSL FAST [31]
April 9, 2015 6pm CNY149-2204 Koene van Dijk Intro to functional connectivity [32]
May 7, 2015 6pm CNY149-2204 Matt Hutchison Brain circuits and functional connectivity
June 18, 2015 6pm CNY149-2204 Christin Sander Intro to positron emission tomography (PET)


Calendar 2013-14:

Date Time Location Speaker Topic References Lecture Slides
September 19, 2013 6pm CNY149-2204 Martin Luessi Intro to Scientific Python [33]
October 3, 2013 6pm CNY149-2204 Sara Sprinkhuizen MR Physics TBD
October 17, 2013 6pm CNY149-2204 Maritza Ebling Intro to FreeSurfer [34]
November 7, 2013 6pm CNY149-2204 Jon Kaiser Intro to Computing at the Martinos Center [35]
November 20 & 21, 2013 6pm Bay 2! Dylan Tisdall Syngo demonstration
January 23, 2014 6pm CNY149-2204 Marco Loggia Neuroanatomy for Dummies [36]
February 6, 2014 6pm CNY149-2204 Jon Kaiser Intro to Launchpad [37]
February 20, 2014 6pm CNY149-2204 Koene van Dijk Resting-state fMRI [38]
March 6, 2014 6pm CNY149-2204 Hari Bharadwaj Statistics
March 20, 2014 6pm CNY149-2204 Jacob Hooker Intro to PET and PET/MRI [39]
April 17, 2014 6pm CNY149-2204 Linda Douw Introduction to Network Theory
April 29, 2014 NB this is a Tuesday! 6pm CNY149-2204 Randy Gollub Grant writing [40]


Calendar 2012-13:

Date Time Location Speaker Topic References Lecture Slides
September 13, 2012 6pm CNY149-2204 Martin Luessi Intro to Scientific Python [41]
September 20, 2012 6pm CNY149-2204 Sam Mehl and Jon Kaiser Intro to Computing at the Martinos Center [42]
October 25, 2012 6pm CNY149-2204 Dylan Tisdall MR Syngo training N/A
November 8, 2012 6pm CNY149-2204 Louis Vinke Intro to FreeSurfer [43]
November 15, 2012 6pm CNY149-2204 Donald McLaren Group Analysis and Its Implications for Experimental fMRI Designs [44]
November 29, 2012 6pm CNY149-2204 Sara Sprinkhuizen MR Physics [45] NB Adobe Flash Player is needed
December 6, 2012 6pm CNY149-2204 Doug Greve Introduction to FsFast N/A
December 13, 2012 6pm CNY149-2204 Sheraz Khan Master MEG/EEG in 45 minutes N/A
--------------
January 10, 2013 6pm CNY149-2204 Martin Luessi Intro to MEG and MNE N/A [46]
January 24, 2013 6pm CNY149-2204 cancelled N/A
February 7, 2013 6pm CNY149-2204 Hari Bharadwaj Introduction to statistics [47]
February 21, 2013 6pm CNY149-2204 Koene van Dijk Resting-state fMRI [48]
March 7, 2013 6pm CNY149-2204 Linda Douw Introduction to network theory [49]
March 12, 2013 NB this is a Tuesday! 6pm CNY149-2204 Randy Gollub Grant writing [50]
April 18, 2013 6pm CNY149-2204 Juliette Selb Intro to NIRS [51]
April 25, 2013 6pm CNY149-2204 Satra Ghosh Nipype N/A



Calendar 2011-12:

Date Time Location Speaker Topic References Lecture Slides
September 29, 2011 6pm CNY149-2204 Khaldoun Makhoul [52] Linux Computing Part I N/A pdf
October 6, 2011 6pm CNY149-2204 Khaldoun Makhoul [53] Linux Computing Part II N/A pdf
October 13, 2011 6pm CNY149-2204 Khaldoun Makhoul [54] MRI Physics I N/A pdf
November 3, 2011 6pm CNY149-2204 Alex Gramfort Python for Matlab users N/A pdf
November 17, 2011 6pm CNY149-2204 Aapo Nummenmaa Matlab N/A pdf
December 1, 2011 6pm CNY149-2204 Dylan Tysdall MRI Syngo Training N/A
December 15, 2011 6pm CNY149-2204 Anna Moore Intro to Molecular Imaging N/A
--------------
January 19, 2012 6pm CNY149-2204 Doug Greve Intro to fsFast N/A pdf
February 2, 2012 6pm CNY149-2204 Louis Vinke Intro to FreeSurfer N/A pdf
February 16, 2012 6pm CNY149-2204 Donald McLaren Rules for Constructing and Reporting Second-level Statistics OrthoView peak_nii 3dClustSim pdf
March 1, 2012 6pm CNY149-2204 Sheraz Khan Master MEG/EEG in one hour N/A pdf
March 22, 2012 6pm CNY149-2204 Marco Loggia Neuroanatomy for Dummies N/A pdf
March 29, 2012 6pm CNY149-2204 Juliette Selb Intro to NIRS N/A pdf
April 5, 2012 6pm CNY149-2204 Martin Luessi Intro to git and github N/A html
April 19, 2012 6pm CNY149-2204 Satra Ghosh {Nipype: ('why', 'what', 'how')} N/A html


Calendar 2010-11:

Date Time Location Speaker Topic References Lecture Slides
October 7, 2010 6pm CNY149-2204 Marco Loggia [55] Neuroanatomy for dummies N/A pdf
October 21, 2010 6pm CNY149-2204 Hari Bharadwaj [56] Statistics N/A pdf
November 4, 2010 6pm CNY149-2204 Donald McLaren [57] The GLM (General Linear Model)-- first and second-level models N/A pdf
November 18, 2010 6pm CNY149-2204 Adrian KC Lee [58] Matlab N/A pdf

review.m

comb.m

comb2.m

factorial.m

factorial2.m

December 2, 2010 6pm CNY149-2204 Khaldoun Makhoul [59] UNIX and basic C shell scripting N/A pdf
February 3, 2011 6pm CNY149-2204 Allison Stevens FreeSurfer N/A pdf
February 17, 2011 6pm CNY149-2204 Jean Chen Arterial Spin Labeling N/A pdf
March 3, 2011 6pm CNY149-2204 Aapo Nummenmaa MEG N/A pdf
March 8, 2011 6pm CNY149-2204 Prof. Randy Gollub [60] Seminar on Grant Writing ppt
March 17, 2011 6pm CNY149-2204 Sheraz Khan [61] PsychToolbox for Stimuli Presentation ppt

.m tutorial

April 7, 2011 6pm CNY149-2204 Dionyssios Mintzopoulos [62] Introduction to R N/A pdf
April 28, 2011 6pm CNY149-2204 Khaldoun Makhoul [63] MR Physics N/A pdf
May 5, 2011 6pm CNY149-2204 Ellen Lau [64] Practical Issues for Multimodal Neuroimaging pdf
May 19, 2011 6pm CNY149-2204 Anastasia Yendiki [65] Introduction to DTI N/A ppt



Calendar 2009-10:

Date Time Location Speaker Topic References Lecture Slides
** Nov 10, 2009 ** 5pm CNY149-2204 Prof. Randy Gollub [66] Seminar on Grant Writing N/A PDF
Nov 19, 2009 6pm CNY149-2204 Adrian KC Lee [67] How to use MATLAB? (Advanced) PDF(m-files) PDF
Dec 3, 2009 6pm CNY149-2204 Hari Bharadwaj [68] Statistics (Beginners) N/A PDF
Dec 17, 2009 6pm CNY149-2204 Hari Bharadwaj [69] Statistics (Advanced) PDF PDF PDF
Jan 14, 2010 6pm CNY149-2204 Allison Stevens [70] Intro to FreeSurfer (Beginners) N/A PDF
Feb 4, 2010 6pm CNY149-2204 Nick Schmansky [71] How do you use Qdec for group analysis of morphometric data? N/A PDF
Feb 18, 2010 6pm CNY149-2204 Lilla Zollei [72] Basic C Shell scripting PDF BOOK PDF
March 4, 2010 6pm CNY149-2204 Marco Loggia [73] By the way, where is the fornix??? An introduction to gross neuroanatomy N/A PDF MOVIE
March 18, 2010 6pm CNY149-2204 Anastasia Yendiki [74] Introduction to DTI analysis N/A PDF
April 1, 2010 6pm CNY149-2204 Aapo Nummenmaa [75] Interpreting MEG data in terms of "distributed sources": under the cover of MNE N/A PDF
April 15, 2010 6pm CNY149-2204 Adrian KC Lee [76] How to navigate through the MEG-MNE workflow? N/A PDF
May 6, 2010 6pm CNY149-2204 -- -- N/A
May 20, 2010 6pm CNY149-2204 Kara Dyckman [77] Where do those pretty colored blobs come from? An introduction to the BOLD signal and fMRI designs. N/A PDF

Beginner's level: No prior knowledge assumed. First exposure or a refresher to the topic.

Advanced level: Prior knowledge assumed. Please check the relevant beginner's level Why.N.How section offered previously for assumed knowledge.

Calendar 2008-09:

Date Time Location Speaker Topic References Lecture Slides
Nov 6, 2008 6pm CNY149-2204 Adrian KC Lee [78] Why do we need to know about Linear Algebra? N/A PDF
Nov 20, 2008 6pm CNY149-2204 Emily Israeli (eisraeli@nmr) How do we use MATLAB? -- an introductory session. N/A PDF ZIP
Dec 4, 2008 6pm CNY149-2204 Lilla Zollei [79] Why do we have so many brain coordinate systems? N/A PDF
Dec 18, 2008 6pm CNY149-2204 Allison Stevens [80] How to use Freesurfer? N/A PDF
Jan 15, 2009 6pm CNY149-2204 Marco Loggia [81] By the way, where is the fornix? An introduction to gross neuroanatomy N/A PDF
Feb 5, 2009 6pm CNY149-2204 Lilla Zollei [82] Intro to basic statistics N/A PDF
Feb 19, 2009 6pm CNY149-2204 Katie Handwerger [83] SPSS tutorial N/A PDF
March 5, 2009 6pm CNY149-2204 Aapo Nummenmaa [84] Why is it called a current dipole? Cohen.PDF PDF1 PDF2
March 19, 2009 6pm CNY149-2204 Daniel Goldenholz [85] How do we analyze MEG data? N/A PDF
April 2, 2009 6pm CNY149-2204 Nick Schmansky [86] How do you use Qdec for group analysis of morphometric data? N/A PDF
April 30, 2009 6pm CNY149-2204 Rudolph Pienaar [87] What is the physics behind MRI? N/A PDF1 PDF2
May 7, 2009 6pm CNY149-2204 Adrian KC Lee [88] Why do we need Signal Processing N How do we conceptualize it? N/A PDF
May 21, 2009 6pm CNY149-2204 Ed Vul [89] Discussion on "Voodoo Correlations" N/A PDF

To facilitate discussion on Ed Vul's paper, we have made the following papers / links available:

Vul et al (2009), "Puzzlingly high correlations in fMRI studies of emotion, personality and social cognition," Perspectives on Psychological Science, 4(3):274-290. (formerly known as "Voodoo Correlations" paper)

Lieberman et al (in press), "Correlations in social neuroscience aren't voodoo: A reply to Vul et al," Perspectives on Psychological Science

Vul et al (2009), "Reply to Comments on 'Puzzlingly high correlations in fMRI studies of emotion, personality and social cognition", 4(3):319-324.

Vul and Kanwisher (in press), "Begging the Question: The Non-Independence Error in fMRI Data Analysis." in Hanson & Brunzl (eds.), Foundations and Philosophy for Neuroimaging.

Jabbi et al, "Response to 'Voodoo Correlations in Social Neuroscience' by Vul et al. - summary information for the press"

Slides from Bob Cox (NIMH) discussion on Voodoo Correlations

For more rebuttals on the Voodoo correlations paper, please visit Ed Vul's website.

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