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Main C-MIND Project Website

Pipeline API Documentation¶

Primary Modules¶

The primary functions for data processing are within the cmind.pipeline module. These are grouped by the type of data processing to which they apply below.

Pipeline Modules Listed by Function¶

Structural Processing Modules¶

`cmind_crop_robust`
`cmind_bias_correct`
`cmind_brain_extract`
`cmind_segment`
`cmind_struct_preprocess`
`cmind_age_to_template`	Choose an age-appropriate pediatric template.
`cmind_normalize`
`cmind_fieldmap_regBBR`
`cmind_rigid_coregister`
`cmind_apply_normalization`
`cmind_atlas_to_subject`
`cmind_calculate_slice_coverage`

CBF Processing Modules¶

`cmind_alpha`
`cmind_baselineCBF_preprocess`
`cmind_baselineCBF_coregisterT1`
`cmind_baselineCBF_quantitative`

Fieldmap Processing Modules¶

cmind_fieldmap_process

Simultaneous ASL/BOLD Modules¶

`cmind_fMRI_preprocess`
`cmind_fMRI_preprocess2`
`cmind_fMRI_outliers`
`cmind_fMRI_level1_stats`
`cmind_fMRI_norm`
`cmind_build_feat_dir`
`cmind_stage_second_level`

T1 Mapping Modules¶

`cmind_T1map_preprocess`
`cmind_T1map_fit`
`cmind_T1_tissue_averages`

DTI/HARDI Modules¶

`cmind_DTI_HARDI_QA`
`cmind_DWI_TRK_to_3plane`

Supporting Modules¶

`globals`	Global variables, pathnames, version information, etc.
`finders`	Utilities to find various external packages
`pipeline.ants_applywarp`	utility for calling antsApplyTransforms
`pipeline.ants_register`	utility for calling antsRegistration
`utils.utils`	Miscellaneous Utilities
`utils.image_utils`	Image Utilities
`utils.file_utils`	File Handling Utilities
`utils.fsf_utils`	FSL .fsf file creation/modification utilities
`utils.logging_utils`	Logging Utilities
`utils.nifti_utils`	NIFTI Handling Utilities
`utils.fsl_mcflirt_opt`	mcflirt motion correction utility
`utils.fsl_mcflirt_opt_ASLBOLD`	mcflirt motion correction for simultaneous ASL/BOLD data
`utils.decorators`	Function decorators
`utils.cmind_HTML_report_gen`	generate HTML reports

Indices and tables¶