Program  in  Cognitive  Affective  Neuroscience (PICAN)

Professor, Department of Psychiatry
University of Pittsburgh School of Medicine

Greg J. Siegle, Ph.D.

Phone: 412-864-3501
Address: Western Psychiatric Institute and Clinic
3811 O’Hara St Pittsburgh, PA 15213 USA

I direct the Program in Cognitive Affective Neuroscience, which has a number of ongoing projects.
I am also on the executive team of the Mood Disorders Treatment and Research Program (MDTRP) which is the clinical trials unit for Western Psychiatric Institute and Clinic. We do our psychotherapy and psychopharmacology studies through the MDTRP.
My lab has opportunities for post-docs as well as undergraduates, and research assistants.

It’s important to me to devote adequate time to mentoring each student in my lab. Due to the large number of students currently affiliated with my lab, this year (2013) I don’t currently intend to consider taking an incoming graduate student for entry in Fall 2014.

My Research

program examines neurophysiological substrates of cognition and emotion in depression and anxiety through the lifespan using self-report, behavioral, physiological, and neuroimaging (fMRI) assessment, as well as computational modeling. A specific goal of this work is to better understand what cognitive and brain processes predict and change with recovery, and how to improve treatments by targeting these mechanisms more directly. The role of sustained emotional information processing (e.g., rumination) is a particular focus of this work. For more detailed information, check out a more detailed description of my research and my vita.

Web-based projects include:

Web-based projects include:
The fMRI Individual Differences Database with contribution instructions.
The Functional Connectivity Toolbox as referenced in Zhou et al (2009) Neuroimage, 47:1590-1607.
Interactive, editable reference list for Neurobehavioral Training and Cognitive Training papers, software, and downloads.
Please feel free to add to this! Also available as pdf snapshot from 10/19/2011.
The Balanced Affective Word List Project and the

Webmaster for: Program in Cognitive Affective NeuroscienceBiometrics Research Program

I received my Ph.D. through the San Diego State University / University of California, San Diego Joint Doctoral Program in Clinical Psychology.

Resources for writing academic papers

Suggested academic
paper outline

This outline is oriented for short-ish submissions to a psychiatry or psychology journal. It also applies to undergraduate and master’s theses in my lab

STROBE checklist

for what to report in cohort, case-control, and cross-sectional studies

CONSORT checklist

for what to report for clinical trials

COBIDAS report

on how to report on fMRI studies

Guidelines papers for psychophysiology

for reporting on psychophysiological studies of all types including heart rate variability, startle, EMG, heart rate, EEG, MEG, ERPs, blood pressure, GSR, etc. They are at the bottom of the page – scroll all the way down.

How To Guides

Academic Pursuits

Writing a draft of a mentor letter about you, from your mentor.

Time-line and some hints for obtaining an NIH K-award is a now-viral document that Judy Ford and I put together for post-docs and junior faculty who are thinking of writing a K-award application. Do not be scared.

Thoughts on writing an F31 NRSA award from Siegle, G.J., Johnson, S. L., Everhart, D.E., Newton, T. (2010). Tips on writing National Research Service Award Predoctoral Fellowship proposals from real NRSA reviewers. The Behavior Therapist, 33, 160-164.

Hints on giving a poster at a conference

Hints on writing a (compassionate) review for a manuscript

Thoughts on interacting with the media

Thoughts on maintaining a hyperfunctional psychology laboratory

Being Borderline – An Operator’s Manual, an unpublished underground how-to guide I wrote for patients in 2000. Most of the information remains current.

Research Life

We get by with a little help from


Software for distribution

Access Database Template

for generating biosketch and University of Pittsburgh School of Medicine CV format lists for grant support. Use the one form (“GrantsInputForm”) to enter grants and then generate one of the 2 reports. The “Grant Table” report is the University of Pittsburgh School of Medicine CV format. The “Grants” report is the standard biosketch format. To export a report to Word format you can use “External Data” –> “More” –> “Word”

Waveform comparisons Matlab code

implements tests to compare physiological waveforms at every sample, as used in a bunch of my lab’s publications. Please install all directories in your matlab path and do check out the documention in the pupil_toolkit_waveform_comparisons.pdf file in the main directory.

Read and Deblink ASL5000

Code to read and deblink ASL5000 pupil data on 64-bit Windows 10 computers running matlab.. This zip file has a pdf that explains how it works and where to install things.

Pupillary waveform deblinking Matlab code

identifies and linearly interpolates through blinks in a waveform of pupillary motility data. Usually works on eyetracking data as well as other relatively physiological waveforms scaled appropriately.

Windsorizing Matlab Code

rescales outliers to the last good value within the Tukey hinges within columns of a matrix.

Software for use in collaboration, not available for download. Not distributed without individual consultation and discussion

My lab uses a great deal of “home grown” software. Many people ask whether they can use it to. The answer is generally yes, but it will take some work. The software is fit for use by engineers or highly trained people, and is not prime-time. It works. It is often not well documented. There are no graphic interfaces. It all takes programming in matlab or Unix scripting. As such, if you are going to request to use it please 1) have a matlab-savvy engineer type on hand (I cannot do tech support) and 2) expect to work closely with me in implementing your stream, at least at first. If you are interested in this type of arrangement, please feel free to talk to me about possible collaboration on your projects. Unfortunately my time is somewhat limited so I cannot afford to distribute this collection of hacks widely. Some of the software libraries we use, and what it would likely take for your group to also use them are described below as examples. Note that I have overengineered the process for getting involved with this code only so that when we are done, we can all be sure that what is coming out of the code is right for your lab.

The Pupil Toolkit.

This is the motly collection of matlab code my lab uses to analyze our pupil data. Typically, using it involves either you visiting my lab or me visiting you for a day or two, working to make sure we can read your data, and process it, and writing example scripts together. This process has worked for many labs.

Emotiv Headset processing code.

This is a collection of Matlab routines built on the FieldTrip and EEGlab matlab platforms. It implements a number of steps for processing data from the Emotiv Headset in a way that ERP and EEG data are interpretable and often comparable to data from much more expensive systems. Publications are forthcoming. It is a work in progress. Typically using it involves entering into a formal collaborative relationship where we are all authors on papers using the code. Site visits are a must.

fMRI code.

This is a collection of scripts, c-source code, and matlab code used by our lab to process our fMRI data. Mostly we work on top of NIS and AFNI. If you want to use our code independently, as we do it, please consider doing a post-doc in my lab. That said, if you are using one of the fMRI tasks developed in my group and want to know whether your results would match ours if you just processed the data like we do, we are frequently up for re-analyzing your data, in collaboration with you.


We are doing research on virtual reality exposure paradigms. Some of these involve zombies. You can see a 360 degree video of our stimuli. Content warning: Our zombies are scary. You can’t shoot them. There are screams and blood and violent expressions. Click here to see our zombies. (works in Chrome, not Firefox…)

Our Research Associate Integrity Agreement is signed by all associates doing research in or with the PICAN lab.
Initial thoughts on using the Emotiv Epoc in research. We’re writing a paper but these are some initial questions people seem to ask a bunch.
Here’s an animation showing the location of the amygdala. Roma Konecky and I made this from an SPGR image acquired on a 1.5T GE scanner using BrainVoyager to align and smooth the image, MRICro to trace the amygdala, AFNI to create the rendering, and WWW Gif Animator to concatenate the frames.

On-line Preprints contains contents or links to some of the papers from my lab. Updated infrequently

The Transdisciplinary Research in Emotion, Neuroscience, and Development (TREND) Artist in Residence Series brings artists and neuroscientists together to answer a question of mutual interest for 1-4 days each year.
Artists – you can apply! We are actively seeking an artist for 2012. To apply, please email Greg Siegle directly with 1) a brief description of a question you have about your art that neuroscience might help to answer and 2) a link to a website where your work can be found.

For inquiring minds:

 For the Siegle et al (2006) American Journal of Psychiatry treatment prediction paper, the BA25 ROI was centered around Talariach coordinates: 6, 17, -6 and extended from 6,17,-2 to 7,19,-11. The Amygdala ROI was maximal at 15,-3,-15 and extended from 13,-3,-14 to 19,-4,-17.

Here’s an animation showing the mean of 25 control participants’ brain activity associated with rating the personal relevance of positive words. The animation was made by generating a snapshot of regions significantly different (p<0.001) from the pre-trial baseline at each TR (1.5 seconds) for the 12 second trial (in AFNI), and interpolating between them (in Virtual Dub). As shown in the animation the anterior cingulate reacts early, followed slightly later by BA47, a brain region associated with rumination. Data from Siegle, G.J., Thompson, W., Thase, M.E., Steinhauer, S.R., Carter, C. S., (in press). Increased amygdala and decreased dorso-lateral prefrontal BOLD responses in unipolar depression: Related and independent features. Biological Psychiatry. Animation by Greg Siegle and Lena Gemmer.

Here are a few interesting mathematical functions I’ve been playing with lately.