~~NOTOC~~

This wiki contains various lab procedures relevant to members of [[http://cfn.upenn.edu/aguirre/ |Geoffrey K Aguirre's Lab]] at the University of Pennsylvania. You must have an account to edit - contact [[aguirreg@mail.med.upenn.edu|Geoff Aguirre]] to have one made. If you are not familiar with [[wiki:syntax|wiki syntax]], please experiment in the [[playground:playground|playground]].
===== People, Publications, Presentations, Resources=====
These pages provide information about the activities and people in the lab.
  * [[lab_people|Lab People]]
  * [[Lab Projects]]
  * [[Lab Publications]]
  * [[Lab Presentations]]
  * [[Lab Resources]]
  * [[public:external_help_links|Getting started in the Aguirre Lab]]
===== Internal Lab Notebooks ===== 
  * [[private:lab_notebooks|Lab notebooks]] PAGELOCKED
  * [[private:Stimulus presentation protocols]] PAGELOCKED
  * [[detrelab:front_page|Link to DetreLab sub-wiki]] PAGELOCKED

===== Places =====
The lab is located within the Hospital of the University of Pennsylvania. These are links to our research sites or sites which we have access to in order to complete research projects on and off campus.
  * [[Directions to the GKA Laboratory]]
  * [[private:chatterjee_lab_experiment_testing_room|Chat lab testing room]] PAGELOCKED
  * [[private:stemmler_434|Stemmler 434]] PAGELOCKED
  * [[private:hup7_at_stellar-chance_labs|7 Tesla scanner]] PAGELOCKED
  * [[private:New Bolton Center (NBC)]] PAGELOCKED
  * [[private:glenolden|Glenolden]] PAGELOCKED
===== Administrative =====
  * [[public:Lab Meeting Schedule]]
  * [[private:phonebook|Phonebook]] PAGELOCKED
  * [[private:certifications|Lab member research certifications]] PAGELOCKED
  * [[private:submitting_and_renewing_irb_and_camris_protocols|Submitting protocols to the IRB and CAMRIS]]PAGELOCKED
  * [[private:currently_approved_protocols|Approved IRB and CAMRIS protocols]] PAGELOCKED
  * [[private:purchasing_supplies_for_the_lab|Purchasing]] PAGELOCKED
  * [[private:grants_and_accounts|Grants and accounts]]PAGELOCKED
  * [[private:software_licenses_in_the_lab|Software licenses]] PAGELOCKED
  * [[private:data_backup|Data backup]] PAGELOCKED
  * [[public:Poster Printing]]
  * [[public:Making a Wiki page private]]
===== Scheduling scans and subjects ===== 
All information relating to scheduling and testing behavioral and fMRI subjects

  * [[private:Using Experimetrix]] (CCN) PAGELOCKED
  * [[private:scheduling_time_and_subjects_on_hup6|Scheduling MRI subjects]] PAGELOCKED
  * [[public:mri_safety_information_and_exclusion_criteria|MRI safety]]
  * [[private:Paying subjects]] PAGELOCKED
  * [[private:Data storage]] PAGELOCKED
===== Stimulus creation ===== 
  * [[private:Creating Faces with GenHead and Sources of Other Face Stimuli]] PAGELOCKED
  * [[private:multidimensional_scaling_and_perceptual_spaces|MDS and perception]] PAGELOCKED
  * [[private:steerable_pyramids|Steerable Pyramids]] PAGELOCKED
  * [[private:gabor_image_similarity|Calculating image similarity with V1-Gabor model]] PAGELOCKED
  * [[public:Radial-Frequency Contours]] (RFCs)
  * [[public:Nakayama Depth Manipulation]] (Bars and Strips)
  * [[http://www.mmrrcc.upenn.edu/CAMRIS/cfn/HupProject.html|HUP6 projector properties and calibration]] with a cached version [[public:HUP6_projector|here]]
  * [[http://platypus.psych.upenn.edu/brainardlabwiki/wikka.php?wakka=OSXMonitorCal|Brainard Lab Wiki OSX monitor calibration]]

===== Continuous Carry-over Designs ===== 
  * [[public:Continuous carry-over for BOLD fMRI|Introduction to carry-over designs]]
  * [[public:M Sequences]]
  * [[public:T1I1 Sequences]]
  * [[public:selection_of_efficient_type_1_index_1_sequences|Selection of Type 1 Index 1 sequences]]
  * [[public:premade_sequences|Pre-made, efficient, T1I1 sequences]]
  * [[public:Generation of continuous carry-over covariates]] 
  * [[public:Example carry-over data and analysis]]
  * [[public:Issue...The effect of the prior neural state vs. the prior stimulus]]

===== MR Imaging Analysis =====
==== Basic MRI data pre-processing ==== 
  * [[public:Links to software packages|Software packages and CPUs on the CfN cluster]]
  * [[public:Location of data on CfN cluster]]
  * [[public:arrangement_of_data_directory]]
  * [[public:downloading_data_from_cd_to_cfn_cluster_and_renaming|Downloading data from CD and renaming]]
  * [[public:standard_prep-script_and_its_components]]
  * [[public:Introduction to the VoxBo scheduler]]
  * [[public:Information on VoxBo file formats]]
  * [[public:Details on pre-processing steps]]
  * [[public:Basic information on the GLM]]
  * [[public:Condition functions]]
  * [[public:Covariates of the G matrix]]
  * [[private:VoxBo script library]] PAGELOCKED
==== Structural ====
  * [[public:Diffusion tensor imaging]]
  * [[private:Canine anatomy analysis]] PAGELOCKED
  * [[private:Freesurfer]] PAGELOCKED
  * [[private:Paraview]] PAGELOCKED

==== Functional/Blood-Oxygen Level Dependent (BOLD) ====
  * [[private:Retinotopic mapping procedures]] PAGELOCKED
  * [[public:perfusion_analysis]]
  * [[public:Distributed pattern analysis]]
  * [[private:creating direct effect and training CUBs]] PAGELOCKED
  * [[public:analysis_of_a_cco_experiment_with_voxbo]]
  * [[private:pulse-oximetry during fMRI scanning]] PAGELOCKED
  * [[private:eye tracking during fMRI scanning]] PAGELOCKED
===== Event-Related Potential (ERP) =====
  * [[private:Description of the Wolk Lab ERP system]] PAGELOCKED
  * [[private:ERP Setup 2 |Running a subject on the Wolk ERP system]] PAGELOCKED
  * [[private:analyzing_erp_data_on_the_cfn_cluster|ERP data analysis under VoxBo]] PAGELOCKED

===== Behavioral / other data =====
  * [[public:pfpb|Philly Face Perceptual Battery (PFPB) Instructions]]
  * [[private:Genetic testing]] PAGELOCKED
 

===== Potpourri =====
  * [[public:Matlab tools]]
  * [[public:useful values|Wandell's useful values]]
  * [[public:Useful shell and perl commands]]
  * [[public:Relevant R Help]]
  * [[public:Excel tricks]]
  * [[http://www.meetingassistant2.com/OHBM2009/planner/abstract_popup.php?abstractno=1742|Why we correct for multiple comparisons]]
[[orphans]]