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| biac:analysis [2013/10/01 15:08] – [Useful Guides] cmp12 | biac:analysis [2014/08/04 16:03] – external edit 127.0.0.1 |
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| ===== Image Analysis software ===== | ===== BIAC Image Analysis software ===== |
| * [[biac:pipeline|Processing Pipeline]] - Automated MRI data transfer and preprocessing 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'') | * [[biac:xmlheader|BXH/XCEDE tools]] - Series of tools for describing imaging data (including ''bxh_eventstats'') |
| * [[biac:freesurfer|FreeSurfer]] - Cortical surface reconstruction software from Harvard University | * [[biac:freesurfer|FreeSurfer]] - Cortical surface reconstruction software from Harvard University |
| * [[biac:fsl|FSL]] - Statistical analysis software from Oxford 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 |
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| ===== Other Analysis software ===== | ===== Other Analysis software ===== |
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| ==Eyetracking analysis== | ====Eyetracking analysis==== |
| * [[jvs:cigal:eyetracking|CIGAL tools]] | * [[jvs:cigal:eyetracking|CIGAL tools]] |
| * [[biac:analysis:ROI_ET|Region Based Analysis]] | * [[biac:analysis:ROI_ET|Region Based Analysis]] |
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| ==Resting State Methods== | ====Resting State Methods==== |
| * [[biac:analysis:resting_pipeline|Python/FSL Resting State Pipeline]] Documentation of the BIAC resting state pipeline | * [[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 | * [[biac:analysis:physiological|Physiological Correction Methods]] Documentation of some local correction methods |
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| ===== Useful Guides ===== | ===== Useful Guides ===== |
| | * **provided by the Huettel Lab** |
| * [[huettel:new_lab_members | Guide for new members]]: Some things to get familiar with | * [[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 |
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| === Data Analysis === | |
| * **thanks to the Huettel Lab for sharing their guides** | |
| * [[huettel:guides_to_data_analysis:2011_FSL_Course|FSL Training Course]]: This page covers training material from FMRIB website. | |
| * [[huettel:guides_to_data_analysis:2011_bootcamp_fmri|Neuro Boot Camp (FMRI Lab)]]: This page covers the lab information for the FMRI Bootcamp. | |
| * [[huettel:FSL_main|FSL]]: FSL is the main analysis package we use in the Huettel lab. | |
| * [[huettel:guides_to_data_analysis:eventstats|Eventstats]]: Eventstats is a BIAC program that is useful for extracting timecourses. | |
| * [[huettel:guides_to_data_analysis:mricron|MRIcron]]: MRIcron is a helpful program for visualizing data and creating impressive figures for manuscripts. | |
| * [[huettel:guides_to_data_analysis:python|Python]] | |
| * [[huettel:guides_to_data_analysis:Misc_main|Misc Analysis Tools]]: This page contains some additional tools for data analysis, for things like ROI generation. | |
| * [[huettel:guides_to_data_analysis:thresholding_lit|Thresholding literature]] | |
| * awi.duhs.duke.edu - VPN password change website - every 180 days! | |
| ===== Download ===== | ===== Download ===== |
| * [[biac:tools|Downloadable Software]] - distribution of BIAC tools freely available for individual use. | * [[biac:tools|Downloadable Software]] - distribution of BIAC tools freely available for individual use. |
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