|
|
|
biac:analysis [2019/02/19 17:15]
cmp12 [TOPUP Correction] |
biac:analysis [2023/02/23 18:43]
|
| ===== 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:analy | |
| * [[biac:analysis:topup_correction|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. | |
| |
