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.
My Research
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 Neuroscience, Biometrics 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
our
P.I.s
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.
Other
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…)
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.