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| | Our website has changed slightly to reflect our new name. The original Visual Brain Core was made possible by a generous grant from UAB's HSF/GEF grant program. Given that our resources ended up being used by a broader base of users than just vision researchers, we've dropped the "visual" from our name. Also, we're continuing our work in collaboration with UAB's Civitan International Neuroimaging Lab, and so we're officially the CINL Brain Core now. |
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| ==Visual Brain Core Mission==
| | Our new website is here: [https://docs.uabgrid.uab.edu/wiki/Brain_Core https://docs.uabgrid.uab.edu/wiki/Brain_Core] |
| Our mission is to help produce high quality, cutting edge research examining the visual brain. To achieve this, we will help investigators overcome some common barriers to performing high quality vision research, and provide forums to discuss new ideas and research techniques. | |
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| [[The 5 aims of the Visual Brain Core]] | | [[File:Core.png|thumb|500px]] |
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| ==Information For Visual Brain Core==
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| ===For Use in Grant Proposals:===
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| [[personnel resources]]
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| [[computing resources]]
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| ===Visual Brain Core Personnel and Office Hours===
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| *Demet Gurler, PhD: Consultation on experimental design and data analysis issues.
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| **'''Office Hours: Tuesday, 2:00 -5:00 pm, Thursday, 9:00 am-12:00 pm, Civitan International Research Center, Room 235C'''
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| We are hiring a [[Computer Systems Specialist]], in conjunction with Research computing.
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| ===Visual Brain Core Seminar Series===
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| Every first Friday, 3:30 PM in CIRC 120.
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| We will discuss new ideas and techniques in brain imaging.
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| [[List of speakers in Visual Brain Core Seminar Series]]
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| [[Past Seminars]]
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| '''Nov 21, 2014''': "White Matter in the Older Brain is More Plastic than in the Younger Brain" Speaker: Yuka Sasaki, PhD, Department of Cognitive, Linguistic and Psychological
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| Sciences, Brown University.
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| '''Jan 9, 2014''' : "UAB Research Computing Resources for Neuroimaging Research" Speakers: John-Paul Robinson, Mike Hanby, Thomas Anthony
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| '''Feb 6, 2015''': "High Gradient Diffusion MRI from the Human Connectome Project" Speaker: Koene Van Dijk, PhD, Department of Radiology, Harvard Medical School.
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| '''March 6, 2015''': "How do we measure functional connectivity? An interactive discussion of functional connectivity methods" Speaker: Kristina Visscher, PhD, University of Alabama at Birmingham.
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| [[Future Seminars]]
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| '''April 3, 2015''': "Generalized Psychophysical Interactions (gPPI): What are they and What they can tell us" Speaker: Donald McLaren, PhD, Department of Neurology, Harvard Medical School.
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| '''May 1, 2015''': TBA
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| ===Other information===
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| [[Protocols in the scanner:]]
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| [[Info about specific processing pipelines implemented on Cheaha]]
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| [[Info about backup resources]]
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| [[Links to info]] about certain most used protocols and software downloads and mailing lists for different software.
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| ==Neuroimaging at UAB==
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| ===UAB Neuroimaging Facilities===
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| [[Civitan Functional Neuroimaging Laboratory]]
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| Director: Mark Bolding, PhD
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| e-mail: mbolding@uab.edu
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| The Civitan Functional Neuroimaging Laboratory (CFNL) is located on the first floor of the Civitan International Research Center at the University of Alabama at Birmingham. It houses a research dedicated Siemens Allegra 3T head-only scanner for structural and functional brain imaging, an MRI preparation room for pre- and post-scan patient monitoring, and a fully-equipped experimental suite for behavioral recording.
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| Single and 4 channel TR head coils are available for use with the Siemens Allegra 3T scanner. Standard Siemens pulse sequences are used in general although some have been modified for research purposes. Triggering signals are available for investigators to synchronize stimulus presentation and behavioral monitoring with scans.
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| The CFNL is equipped with an IFIS-SA system for audio/visual stimulation. Visual stimulus presentation can be delivered using an advanced fiber optic system (IFIS-SA) or using back-projection with an LCD projector and a screen at the end of the patient table.
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| Auditory stimuli are presented using a pneumatic headphone system (IFIS-SA). Behavioral measurement can be accomplished using IFIS-SA button response units or fORP joystick and button boxes. Cardiac and respiratory functions can be monitored using an Invivo remote physiological monitoring system. In addition, Eyelink equipment and software is available for eyetracking during scanning.
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| Scans available: Functional (BOLD) MRI, Diffusion Tensor Imaging, Magnetic Resonance Spectroscopy, as well as other traditional T1 and T2-weighted structural scans.
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| Equipment
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| 3T Siemens Allegra MRI scanner
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| Center Affiliation
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| Civitan International Research Center
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| Serving - UAB Internal and External
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| [[UAB-HSF MEG Laboratory]]
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| [[Small Animal Imaging Shared Facility]]
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| Equipment for collecting behavioral data during Neuroimaging
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| *[http://www.sr-research.com/EL_1000.html Eye Tracker]
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| ===Neuroimaging and Systems Neuroscience Labs at UAB===
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| *[http://www.markbolding.com/ Bolding Lab]
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| *[http://www.uab.edu/cbra/ Kana Lab/Cognition, Brain, and Autism Laboratory]
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| *[http://www.uab.edu/cas/psychology/psy-fac/33-primary-faculty/48-dr-david-knight Knight Lab]
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| *[http://labs.uab.edu/kwon/ Kwon Lab]
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| *[http://www.uab.edu/medicine/psychiatry/faculty/faculty-bios/78-adrienne-c-lahti Lahti Lab]
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| *[http://www.uab.edu/medicine/neurology/faculty/a-z/szaflarski Szaflarski Lab]
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| *[http://visscher.neurobiology.uab.edu/Home.html Visscher Lab]
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| *[http://www.psy.uab.edu/younger/ Younger Lab/Neuroinflammation, Pain and Fatigue Laboratory]
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| ===Cluster Computing Environment at UAB: Cheaha===
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| * [[Cheaha_GettingStarted]] - information on getting an account and learning about how to use the cluster
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| * [[Cheaha]] - background information on the cluster useful for grants and publications
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| ===UAB-Auburn University Collaboration for Neuroimaging===
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| '''[http://www.eng.auburn.edu/research/centers/mri/ Auburn University MRI Research Center]'''
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| '''[http://www.eng.auburn.edu/research/centers/mri/equipment/siemens-magnetom-7t.html Siemens Magnetom 7T]'''
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| '''UAB & Auburn Neuroimaging Journal Club'''
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| *Neuroimaging journal Club. Every other Friday at noon, second floor CIRC. Contact Adrienne Lahti to get on the mailing list alahti@uab.edu
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| '''[[UAB & Auburn Neuroimaging Retreat]]'''
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| [[Photos]]
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| ==How To...==
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| ===Computer and coding related how-to's===
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| [[Using Linux]]
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| [[Matlab]]
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| [[Psychtoolbox]]
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| [[Coding Help]]
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| *[[Unix shortcuts]]
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| *[[Eye Tracker]]
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| ===fMRI related how-to's and important links===
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| [[General Information]]
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| [[Tools]]
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| [[Brain atlases]]
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| [[Cool Websites for Beginners]]
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| [[fMRI statistics]]
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| ===UAB Neuroimaging Tools and How-To's (requires blazer id)===
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| [[Imaging Protocols]]
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| [[Analysis Scripts]]
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| [[Behavioral data analysis techniques]]
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| [[Institutional Review Board]]
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