===== BIAC Image Analysis software =====
  * [[biac:pipeline|Processing Pipeline]] - Automated MRI data transfer and preprocessing software.
  * [[biac:xmlheader|BXH/XCEDE tools]] - Series of tools for describing imaging data (including ''bxh_eventstats'')
  * [[jvs:fscan|fScan]] - fMRI visualization and analysis.
  * [[biac:matlab|MATLAB Tools and Guides]]
    * [[biac:matlab:help|Working with MATLAB]] - A brief overview of how to use MATLAB, including basic syntax, working with variables, and using scripts, functions, and programs.
    * [[biac:matlab:showsrs2|showsrs2]] - Matlab tool for viewing of fMRI data.
    * [[biac:matlab:tstatprofile|Tstatprofile]] - Matlab function for event-related fMRI data (deprecated in favor of bxheventstats).

==== BIAC support for other imaging software packages ====
  * [[biac:spm|SPM]] - Statistical Parametric Mapping software from the University of London
  * [[biac:freesurfer|FreeSurfer]] - Cortical surface reconstruction software from Harvard University
  * [[biac:fsl|FSL]] - Statistical analysis software from Oxford University
  * [[biac:dtiprep|DTIPrep]] - DTI QA and preprocessing software from NRRD
  * [[biac:dtk|DTK]] - Diffusion ToolKit for DTI analysis from Harvard
  * [[biac:medinria|MEDInria]] - DTI analysis from France

===== Other Analysis software =====
  
====Eyetracking analysis====
    * [[jvs:cigal:eyetracking|CIGAL tools]] 
    * [[biac:analysis:ROI_ET|Region Based Analysis]]

====Resting State Methods====
  * [[biac:analysis:resting_pipeline|Python/FSL Resting State Pipeline]] Documentation of the BIAC resting state pipeline
  * [[biac:analysis:physiological|Physiological Correction Methods]] Documentation of some local correction methods

====Structural Connectome Methods====
  * [[biac:analysis:structural_connectome|Structural Connectome Pipeline]] Documentation of basic structural connectome methodology

====TOPUP Correction====
  * [[biac:analysis:topup_correction#epi_correction_with_polarity_images_using_topup|EPI Correction]] with polarity images using TOPUP
  * [[biac:analysis:topup_correction#dwi_correction_with_b0s_using_topup|DWI Correction]] with B0s using TOPUP


===== Useful Guides =====
  * **provided by
 the Huettel Lab**
  * [[huettel:new_lab_members | Guide for new members]]: Some things to get familiar with
  * [[huettel:guides#guides_to_data_analysis | Guides for data analysis]]: ( FSL Course, Neuro Boot Camp, Eventstats, mricron, python, misc tools, thresholding )
  * [[huettel:guides#guides_to_stimulus_presentation | Guides for stimulus presentation software]]: ( CIGAL, PsychtoolBox, Optseq2 ) 
  * [[huettel:guides#guides_to_running_subjects | Guides for running subjects]]: Information about running subjects
  * [[huettel:guides#matlab_tools_and_tricks | Matlab info]]: Useful information and common issues while running matlab

===== Download =====
  * [[biac:tools|Downloadable Software]] - distribution of BIAC tools freely available for individual use.