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biac:analysis [2013/10/01 16:02] – [Useful Guides] cmp12 | biac:analysis [2019/02/19 17:14] – [TOPUP Correction] cmp12 |
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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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| ====Structural Connectome Methods==== |
| * [[biac:analysis:structural_connectome|Structural Connectome Pipeline]] Documentation of basic structural connectome methodology |
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| ====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 |
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===== Useful Guides ===== | ===== Useful Guides ===== |
* **provided by the Huettel Lab** | * **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_to_data_analysis | Guides for data analysis]]: ( FSL Course, Neuro Boot Camp, Eventstats, mricron, python, misc tools, thresholding ) | * [[huettel:guides#guides_to_data_analysis | Guides for data analysis]]: ( FSL Course, Neuro Boot Camp, Eventstats, mricron, python, misc tools, thresholding ) |
* [[huettel:guides_to_stimulus_presentation | Guides for stimulus presentation software]]: ( CIGAL, PsychtoolBox, Optseq2 ) | * [[huettel:guides#guides_to_stimulus_presentation | Guides for stimulus presentation software]]: ( CIGAL, PsychtoolBox, Optseq2 ) |
* [[huettel:guides_to_running_subjects | Guides for running subjects]]: Information about running subjects | * [[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 ===== | ===== 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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