===== Data collection and analysis =====
We provide information regarding our methods for our published work. Methods pages that are not public are indicated by a lock symbol.

==== Basic MRI data pre-processing ==== 
  * [[cfn_cluster|The CfN cluster -- software and CPUs]]
  * [[location_of_data_on_cfn_cluster]]
  * [[arrangement_of_data_directory]]
  * [[downloading_data_from_cd_to_cfn_cluster_and_renaming|Downloading data from CD and renaming]]
  * [[standard_prep-script_and_its_components]]
  * [[introduction_to_the_voxbo_scheduler]]
  * [[information_on_voxbo_file_formats]]
  * [[details_on_pre-processing_steps]]
  * [[basic_information_on_the_glm]]
  * [[condition_functions]]
  * [[covariates_of_the_g_matrix]]
  * [[private:voxbo_script_library]]

==== Structural ====
  * [[diffusion_tensor_imaging]]
  * [[private:canine_anatomy_analysis]]
  * [[private:freesurfer]]
  * [[private:paraview]]
  * [[private:diffeomorphic_prep.vbp|Calculation of diffeomorphic warp for VBM analysis]]
  * [[private:B0_field_map_unwarp|Collection of B0 image and EPI un-warping]]

==== Functional/Blood-Oxygen Level Dependent (BOLD) ====
  * [[private:retinotopic_mapping_procedures]]
  * [[private:receptive_field_mapping_procedures]]
  * [[distributed_pattern_analysis]]
  * [[private:creating_direct_effect_and_training_cubs]]
  * [[analysis_of_a_cco_experiment_with_voxbo]]
  * [[pulse-oximetry_during_fmri_scanning]]
  * [[eye_tracking_during_fmri_scanning]]
  * [[private:group_statistical_analysis_with_spherical_atlas]]