- Beginners in ZLAB
- Experimental Design
- EEG/ERP Experiments
- Data analysis and publications
- Tools and General Skill Sets
- Grant Application
Reading materialsFor ERP research, we recommend Dr. Steve Luck's book. The pdf files for each chapter are available on the shared lab folder. The printed book is also available in the lab.
Online short EEG tutorial videos for beginners
Practice basic electrode positioning with the international 10-20 system
Drag the electrode label circle to the intended position on scalp. If you did it right, the label would stay on the head.
A full documentary about top secrets of the brain
- Data collection training. We do training for our students during real experiments. Please check lab calendar for scheduled experiments online.
- Data analysis training. Please schedule individual training sessions with the lab manager or senior lab member.
- Templates for conference posters and journal manuscript preparation are available to lab members.
EEG and MEG experiments
EEG/ERP research in Zhang Lab, Room 119I, Shevlin Hall.
MEG research in Magnetic Source Imaging Lab at United Hospital, St. Paul.
Collaborator: Dr. Wenbo Zhang
MEG work at Research Center for Advanced Technologies at Tokyo Denki University.
Collaborators: Dr. Iku Nemoto, Dr. Masaki Kawakatsu, Dr. Keita Tanaka, Dr. Atsushi Aoyama
- Oddball paradigms
- Stroop paradigms
- Syntactic and semantic violation paradigms
- Audiovisual and cross-modal paradigms
- Priming paradigms
- Random block designs
fMRI/MRI experiments at CMRR
Students: Sharon Miller, Tess Koerner, Luodi Yu
Collaborators: Dr. Phillip Burton and Dr. Cheryl Olman
- Block designs
- Event-related designs
- Speech and sound synthesis
- Klatt Formant Synthesizer
- STRAIGHT synthesis in Matlab
- Sony SoundForge
- Acoustic analysis
- Audio and video recording and editing
- HD Canon camcorder combined with high-quality audio recording with Presonus Firebox and professional microphones.
- Audio and video editing using Final Cut Pro and Sony SoundForge.
- NBS Presentation
- ANT eevoke
- Visual C++
- E-prime 2.0 Professional
Zhang Lab uses all the tools listed here.
- Subject condition. Subjects should be comfortable, relaxed, vigilant and awake (eyes open) during EEG recording. Tense and nervous people cannot be good subjects. Drowsy condition is bad for data recording. Medications can affect the data as well.
- EEG signal. The EEG signals recorded from the scalp are extremely weak. They can be contaminated by artifacts from biological sources (eye blinks, eye browse movement, head movement, neck muscular tension, facial muscular movement, biting, chewing, heartbeat, etc.), environmental sources (low-frequency electromagnetic interference such as the AC powerline, high-frequency electromagnetic interference, mechanical vibrations, etc.), and chemical and physical substances in the subject's hair (hair styling products, magnetic dust particles, static charge buildup, etc.)
- Communication. Perform as a confident professional researcher and communicate well with subjects.
- Introduce yourself and the experiment.
- Ask subjects to read the consent form and remind them to ask questions before obtaining signature.
- Talk to subjects before experiment, in between recording sessions, and after experiment.
- If subject feels sleepy, restless, upset, or in bad physical or mental condition, rescheduling or canceling is a better option.
- Problems and trouble shooting. If there are problems in EEG recording that cannot be resolved, seek help immediately (dial office phone 4-7818 or call Yang Zhang's cell phone directly). Take notes in Experimental Record file and post them on the lab forum online. The Lab Forum on the Zhang Lab in SLHS web site will automatically generate a notice of the issue and send it to lab manager.
- HIPAA and CITI training. EEG/ERP operators must be trained and approved by lab manager before running subjects independently.
- Reminder for participant.
- Send reminder at least one day before experiment. (Remind them to have a good sleep the night before the study.)
- Recommendations: 1. Avoid hair styling products. 2. Wear 100% cotton clothes.
- Statics and other interferences. Metal pieces (such as keys) and electronic devices (such as MP3, cell phone) on the subjects should be kept in the locker in the control room during experiment.
- Booth fan and power circuit. Turn off the fan and power circuit in the booth before data collection.
- Preparation 1. Make sure the caps, gel, syringes, needles are ready. Check if any of the gel-holding caps on each electrode is missing and make sure each electrode (the metal bit) looks clean. If the metal bits do not look clean, clean the electrode(s) using alcohol towelette and Q-tips.
- Preparation 2. Get tissue paper, towels, consent forms, debriefing forms, questionnaire ready. If movie watching is used, make sure the DVD can play and is appropriate in content.
- Preparation 3. Generate Experimental Recording file for the subject and generate subject ID according to the lab manual.
- Impedance and Gel. 1. Applying alcohol towelette for cleaning electrode sites on scalp, including Fp1, Fpz, Fp2, M1, M2, T7, T8, C5, and C6 is recommended before cap fitting. 2. Shake the gel container well before applying. 3. Avoid too much gel for each electrode (especially the ground channel).
- 60 Hz interference (How to reduce it if there is noticeable 60 Hz noise on the recording screen?)
1. Subject's feet must be off the floor. (Rest feet on the foot stool.)
2. EEG cables connections. Make sure the cable connection to the EEG amplifier is good.
3. Use the right amount of gel for the ground channel. (Not too much, not too little; avoid gel on ground channel spreading to neighboring channels!)
4. Statics may build up during sessions longer than 20 minutes, making the subject more susceptible for electromagnetic interferences. (Use the static discharge pad.)
5. Turn off all the circuits in the booth (Use the main switch inside the booth close to the door; all devices are powered through outside the booth).
6. Avoid moving the monitor too close to the subject. Allow at least 1.2 meters distance.
- Trigger codes: All desired trigger codes (including behavioral response codes where applicable) should show up on the recording screen. Otherwise, stop the experiment.
Artifacts can arise from a number of sources, including eyeball movement, blinks, head movement, sweating, swallowing, tension in the neck and body, excessive movement when pressing a button, boredom alpha waves, etc.
1. Subjects must keep their eyes open during data recording unless the specific condition requires closing eyes.
2. Remind subjects to avoid excessive blinking and eyeball movement. (Avoid contact lenses, build blink breaks in the experiments, talk to the subject about blinking artifact and show the artifact before experiment.)
3. Remind subjects to refrain from chewing, biting, swallowing, and other bodily movements. (relax, adjust to a comfortable position, open mouth slightly, etc.)
4. Finger movements for behavioral responses should not show noticeable EEG waveform changes.
5. Abnormal spikes may indicate sudden movements, dried up gel, and static buildup/discharge.
6. Check impedance after a recording session of 10 minutes or longer. Fix impedance issues before recording.
7. To minimize boredom alpha waves, ask subject to get good sleep the day before the experiment, run short blocks (talk to the subjects in between blocks), vary ISI, use + sign for eye fixation during listening, etc. Allow longer breaks in between recording sessions longer than 15 minutes, remind the subject to readjust position, and stretch arms and legs, before going to the next recording session.
- Trouble shooting.
Refer to the lab manuals for trouble shooting or ask for help by calling Zhang's office at 4-7818 or cell phone from the control room.
- Follow these steps (Training is required before operating any device in Zhang Lab)
- Subject consent procedure.
- Cap selection procedure. Measure the subject's head size using special tape. Enter the head size information on Experimental Record file.
- Cap fitting procedure.
- Electrode 3D digitization procedure (only used for those experiments with hypotheses about source localization)
- Gel filling and impedance check procedure.
- Presentation calibration procedure for auditory and visual stimuli. Measure hearing threshold, and adjust sound presentation level, monitor position, speaker position, etc.
- Stimulus presentation and data recording.
- For auditory and visual experiments, do not skip the screening tests using 1k Hz tone and visual checkerboard.
- Note taking. Watch the data recording and picture-in-picture subject-monitoring screen and take notes about subject's behavior and the online EEG waveforms. Make sure the trigger markers are showing up appropriately. If not, check the cable connections between stimulation computer, EEG amplifier, response keyboard, and acquisition computer.
- Breaks for subject. Long session of data recording needs breaks. Providing drinking water to subject can help. Talk to subject through intercom between sessions.
- Complete Experimental Record file.
- Data backup (including experimental record file, and electrode digitization file, if applicable; either one local copy on the USB hard disk or one copy on lab server if you know the password for the server.)
- Clean up. Chair, desk, syringes, blunt needles.
- Assist hair washing for subject.
- EEG cap washing. Click here for instructions from the manufacturer.
- Laundry. Remind lab manager about laundry for the towels if they are about to be used up.
- Turn booth fan back on
- Turn off computers, main power switch in control room and all lights.
- Securely lock all the doors before leaving.
- Send an appreciation note to subject from ude.nmu|balgnahz#ude.nmu|balgnahz using the lab gmail account.
- Designated computer in the EEG control room should be used for data analysis. Do not use acquisition and stimulation workstations for analysis unless you have permission from Dr. Yang Zhang.
- Seek tutorials and training for analysis in ASA and Excel from lab manager.
- Use template forms in Excel.
- Use Systat12 for statistical analysis.
- For graphics, use Ms Excel, Photoshop and Illustrator.
- ZLAB users are recommended to use Matlab functions and scripts to do data analysis. Please consult Yang Zhang for help in doing analysis and graphics if needed.
EEG-ERP analysis tutorials
MRI Safety Manual
fMRI analysis and tutorials
- Basic information for using the 3T MRI facility at CMRR.
- For fMRI data, AFNI and BrainVoyager scripts are available on the Mac computer.
- Basic fMRI analysis procedure: data conversion -> preprocessing (motion correction, T1-T2 alignment, etc., time shifting) -> individual subject analysis -> post processing (clustering, etc.) -> group analysis -> other analysis of interest (ROI, connecitivity)
- 1. Identification of outlier voxels in functional dataset
- 2. Creation of censor files to remove bad datapoints from analysis
- 3. Time shifting
- 4. Volume registration
- 5. Alignment of functional dataset with anatomical dataset
- 6. Creating a mask to clip non-brain voxels
- 8. Despiking functional data
- 9. Deconvolution (Regression) analysis
- 10. Scaling and Extraction of % signal change
- 11. Blurring
- 12. Transformation to Talairach space
- 13. Between-groups (conditions) statistical tests
- 14. Clustering and thresholding
- 15. Region of interest (ROI) analysis
- 16. Finally… Preparing colorful brain activity maps…
- Overview of fMRI analysis by S M Smith.
- fMRI_user_guide by Michael Yassa.
- Another conceptual guide by Bianca de Haan and Chris Rordon based on SPM software.
- ASA4.7 scripts and BESA scripts for EEG data analysis. AFNI and BrainVoyager scripts for fMRI data analysis.
- Matlab scripts are routinely developed for data analysis as part of Zhanglab Toolbox in conjunction with EEGLAB, Fieldtrip, MNE, etc..
- MEG analysis using Neuromag software
- MEG analysis using Fieldtrip
- EEG/ERP analysis using EEGLAB
- EEG/ERP analysis using BESA
- EEG/ERP analysis using ASA
- fMRI analysis using BrainVoyager
- fMRI analysis using AFNI
- Matlab file exchange
- Use Endnote software for references on analysis workstation. Each paper should have its own Endnote library file.
- Ask Tess Koerner for templates if needed.
- Consult with Dr. Zhang for co-authorship, appropriate acknowledgment and journal selection.
- Seek approval from PI and collaborators before submission. In general, the cover letter would be signed by the PI of the project.
Sample auditory and visual ERP data
NOTE: If your ERP data for auditory/visual stimuli do not resemble the sample data in terms of N1/P2 complex on the individual subject level, there are probably problems that should be fixed before doing more data collection for the study.
- ERP for auditory 1 kHz tone; single adult subject; lowpass at 40 Hz; 126 good trials.
- ERP for visual checkerboard; single adult subject; lowpass at 40 Hz; 112 good trials.
Post message on ZLAB forum
Researchers need to learn a number of important tools for studies in Zlab.
Themes and topics online
- General Issues in Child Language Development
- Auditory list home page
- Bishop Blog - insightful discussions on language and language disorders
- Talking brain blog by leading scientists, David Poeppel and Greg Hickok
- Discussions on cognitive neuroscience
- Inside the teenage brain, a Frontline program by PBS
- Matlab. Familiarity with matlab programming and graphics is very helpful.
- Linux/Unix. Basic commands for running analysis in Unix environment is helpful.
- Statistics. Familiarity with Systat, Excel, and SPSS or other software packages is helpful.
- Graphics. Editing with Photoshop and Illustrator.
- Stimulus-related software. Praat, E-prime, NBS Presentation, EEvoke, Matlab.
- BrainImaging software. AFNI, BrainVoyager, BESA, ASA, EEGLAB, Fieldtrip, SPM8, etc.
- Writing & Presentation. Being a good writer and presenter is essential to one's success in a scientific career.
Consult with Dr. Zhang for ZLAB toolbox, reference books, manuals, and tutorials.
Software development in Zhang Lab
- New phonetic training software is currently being tested in two collaborative studies in China. This software uses a new database design for data collection and audiovisual exaggeration in adaptive listening. It is based on the software used in Zhang et al. 2009.
- New matlab routines for EEG analysis (ANT .cnt format) and MEG (Neuromag .fif format) analysis using MNE2.6 have been developed with the help from Dr. Matti Hämäläinen.
- Statistical routines in matlab for MCE analysis in MEG (Neuromag .fif format) have been developed.
- Matlab programs are routinely developed to analyze behavioral, EEG, MEG and fMRI data. These programs are for specific projects, especially for speech synthesis and EEG and MEG analyses. See Zhang et al. 2005 and Zhang et al. 2009 for specific examples in MEG studies.
- Praat scripts are developed for acoustical analysis, simple experiments such as goodness rating and speech synthesis. Experiments that require reaction time measures are programmed in Eevoke, Matlab, E-prime, and NBS Presentation.
- National Science Foundation
- National Institute of Health
- The Dana Foundation
- McKnight Neuroscience Grants
Student Grant and Scholarship Opportunities
Please consult with Dr. Zhang for student opportunities. In the past, many undergraduate and graduate advisees in ZLAB have won distinguished awards at the college, university, national, and international levels.
- Log in to Google lab calendar for meeting schedules.
- Suggest ideas for discussion and meeting by writing to ude.nmu|balgnahz#ude.nmu|balgnahz.
Consulting and collaborations
- Members/collaborators: Please use the online member forum for Q and A before asking for an appointment with lab manager or Dr. Zhang.
- For students and researchers who seek technical consulting and collaboration opportunities, please write to Zhang Lab in SLHS at ude.nmu|balgnahz#ude.nmu|balgnahz. Depending on time availability and interest match, we may not be able to provide consulting or technical support to you.
- CLA Brain Imaging Scientist, Dr. Phillip Burton, would be a good resource for those who work at University of Minnesota.