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biac:analysis [2013/10/01 16:01]
cmp12 [Useful Guides] 		biac:analysis [2019/02/19 17:15]
cmp12 [TOPUP Correction]
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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'')
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   * [[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
  
 ===== Other Analysis software ===== ===== Other Analysis software =====
      
-==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]]
  
-==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
  
-===== Useful Guides =====+====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: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.
  
biac/analysis.txt · Last modified: 2023/02/23 18:43 (external edit)

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