More derivatives documentation

Author: jpellman

docs/user/_sources/_static/outputs/derivatives.csv

@@ -1,5 +1,5 @@
 All Outputs
-#TODO Find out the names given to derivatives in cpac_pipline.py
+#TODO Find out the names given to derivatives in cpac_pipeline.py
 <derivative>_zstd, The z-score standardized output for a derivative.
 <derivative>_fisher_zstd - The z-score standardized output for a derivative using Fisher's z-score transformation.
 output_means, A directory containing a series of nested sub-directories of the following form (with subdirectories representing optional steps only included if those steps were run): _scan_rest/_csf_threshold_<threshold>/_gm_threshold_<threshold>/_wm_threshold_<threshold>/<nuisance_regressors>/_hp_<high frequency cut-off>/_lp_<low frequency cut off>/.  At the lowest level of these subdirectories are text files that contain the average values for each derivative run.  These individual means are also aggregated into a single file of the form 'output_means_<subject name>.csv' in the individua subject output directory.
@@ -9,13 +9,13 @@ Smoothing
 <derivative>_smooth,  directory containing a series of nested sub-directories of the following form (with subdirectories representing optional steps only included if those steps were run): _scan_rest/_csf_threshold_<threshold>/_gm_threshold_<threshold>/_wm_threshold_<threshold>/<nuisance_regressors>/_hp_<high frequency cut-off>/_lp_<low frequency cut off>/_fwhm_<kernel_fwhm>.  At the lowest level of these subdirectories are smoothed NifTI files.
 
 Seed-based Correlation Analysis (SCA) - Analyze the connectivity between brain regions.
-sca_roi_correlation_files
-sca_roi_correlation_stack
-sca_seed_correlation_files
-sca_tempreg_maps_files
-sca_tempreg_maps_stack
-sca_tempreg_maps_zstat_files
-sca_tempreg_maps_zstat_stack
+sca_roi_correlation_files, The results of seed-based correlation analysis for extracted time series from ROIs using 3dTcorr1D.  Results for multiple ROIs are contained in separate files. (?)
+sca_roi_correlation_stack, The results of seed-based correlation analysis for extracted time series from ROIs using 3dTcorr1D.  Results for ROIs are concatenated together into a single 4D NifTI file. (?)
+sca_seed_correlation_files, The results of seed-based correlation analysis for extracted time series from seed specifications using 3dTcorr1D.
+sca_tempreg_maps_files, The results of multiple regression seed-based correlation analysis for extracted time series from ROIs.  GLM parameter estimate images for each timeseries in the input file. Results for multiple ROIs are contained in separate files. (?)
+sca_tempreg_maps_stack, The results of multiple regression seed-based correlation analysis for extracted time series from ROIs.  GLM parameter estimate images for each timeseries in the input file. Results for ROIs are concatenated together into a single 4D NifTI file. (?)
+sca_tempreg_maps_zstat_files, The z-standardized results of multiple regression seed-based correlation analysis for extracted time series from ROIs.  GLM parameter estimate images for each timeseries in the input file. Results for multiple ROIs are contained in separate files. (?)
+sca_tempreg_maps_zstat_stack, The z-standardized results of multiple regression seed-based correlation analysis for extracted time series from ROIs.  GLM parameter estimate images for each timeseries in the input file. Results for ROIs are concatenated together into a single 4D NifTI file. (?)
 
 Dual Regression - Compare large-scale networks.
 spatial_map_timeseries
@@ -26,14 +26,14 @@ dr_tempreg_maps_zstat_stack
 
 Voxel-mirrored Homotopic Connectivity (VMHC) - Investigate connectivity between hemispheres.
 vmhc_fisher_zstd_zstat_map
-vmhc_raw_score
+vmhc_raw_score, The VMHC results in a 3D NifTI file.
 
 Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (fALFF) - Measure the power of slow fluctuations in brain activity.
-alff_img
-falff_img
+alff_img, The ALFF results in a 3D NifTI file.
+falff_img, The f/ALFF results in a 3D NifTI file.
 
 Regional Homogeneity (ReHo) - Measure the similarity of activity patterns across neighboring voxels.
-raw_reho_map
+raw_reho_map, The results for ReHo in a 3D NifTI file.
 
 Network Centrality - Analyze the structure of functional networks.
-centrality_outputs
+centrality_outputs, A directory containing degree centrality, eigenvector centrality, and lfcd results as NifTI files.