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.
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.
cmind_alpha |
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cmind_baselineCBF_preprocess |
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cmind_baselineCBF_coregisterT1 |
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cmind_baselineCBF_quantitative |
cmind_fieldmap_process |
cmind_fMRI_preprocess |
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cmind_fMRI_preprocess2 |
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cmind_fMRI_outliers |
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cmind_fMRI_level1_stats |
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cmind_fMRI_norm |
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cmind_build_feat_dir |
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cmind_stage_second_level |
cmind_T1map_preprocess |
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cmind_T1map_fit |
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cmind_T1_tissue_averages |
cmind_DTI_HARDI_QA |
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cmind_DWI_TRK_to_3plane |
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 |