Documenting derivatives

Author: jpellman

docs/user/_sources/_static/outputs/anatomical/segmentation.csv

@@ -1,6 +1,6 @@
-anatomical_csf_mask, The CSF mask produced by segmentation.
-anatomical_gm_mask, The gray matter mask produced by segmentation.
-anatomical_wm_mask, The white matter mask produced by segmentation.
+natomical_csf_mask, The CSF mask(s) produced by segmentation.  NifTIs are contained within a subdirectory of the form _csf_threshold_<threshold>.
+anatomical_gm_mask, The gray matter mask(s) produced by segmentation.  NifTIs are contained within a subdirectory of the form _gm_threshold_<threshold>.
+anatomical_wm_mask, The white matter mask(s) produced by segmentation.  NifTIs are contained within a subdirectory of the form _gm_threshold_<threshold>.
 seg_mixeltype, A mixeltype volume file (an output from brain segmentation using FAST).
 seg_partial_volume_files, Partial volume estimate files (outputs from brain segmentation using FAST).
 seg_partial_volume_map, The partial volume file (an output from brain segmentation using FAST).

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

@@ -0,0 +1,39 @@
+All Outputs
+#TODO Find out the names given to derivatives in cpac_pipline.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.
+<derivative>_to_standard, A derivative transformed into MNI space.
+
+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
+
+Dual Regression - Compare large-scale networks.
+spatial_map_timeseries
+dr_tempreg_maps_files
+dr_tempreg_maps_stack
+dr_tempreg_maps_zstat_files
+dr_tempreg_maps_zstat_stack
+
+Voxel-mirrored Homotopic Connectivity (VMHC) - Investigate connectivity between hemispheres.
+vmhc_fisher_zstd_zstat_map
+vmhc_raw_score
+
+Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (fALFF) - Measure the power of slow fluctuations in brain activity.
+alff_img
+falff_img
+
+Regional Homogeneity (ReHo) - Measure the similarity of activity patterns across neighboring voxels.
+raw_reho_map
+
+Network Centrality - Analyze the structure of functional networks.
+centrality_outputs

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

@@ -1,26 +1,26 @@
 Functional Preprocessing
+slice_time_corrected
+raw_functional
 coordinate_transformation
 functional_brain_mask
 functional_brain_mask_to_standard
 functional_freq_filtered
-functional_median_angle_corrected
 functional_mni
-functional_nuisance_residuals
 functional_preprocessed_mask
 functional_to_anat_linear_xfm
-preprocessed
-raw_functional
 mean_functional
 mean_functional_in_anat
 mean_functional_in_mni
 selected_func_volume
-slice_time_corrected
 itk_collected_warps_%s
 itk_func_anat_affine_%s
+preprocessed
 
 Nuisance Corrections
 motion_correct
 motion_correct_to_standard
+functional_median_angle_corrected
+functional_nuisance_residuals
 
 Temporal Filtering
 bandpassed_file