C-PAC Output Directory Layout

A standard C-PAC run output directory for one participant-session is shown below. A directory like this will exist for each participant-session in the run.

This is with all derivatives enabled, and the output, smoothing, and z-scoring options all at “Default”:

_images/output_dir_default.png

Output Descriptions

  • alff_to_standard_smooth_zstd: Warped to standard template, smoothed, z-score standardized output of ALFF.
  • anatomical_brain: Skull-stripped brain in anatomical space. This is the direct output of skull-stripping.
  • anatomical_csf_mask: Binary mask of the CSF in anatomical space. This is a result of anatomical segmentation.
  • anatomical_gm_mask: Binary mask of the gray matter in anatomical space. This is a result of anatomical segmentation.
  • anatomical_reorient: Deobliqued, reoriented whole-head anatomical scan. No other pre-processing yet.
  • anatomical_to_mni_nonlinear_xfm: Nonlinear warp transform from anatomical space to template space. Either ANTS or FSL-FNIRT warp depending on which was used.
  • anatomical_to_standard: Anatomical whole-head scan warped to standard/template.
  • anatomical_to_symmetric_mni_nonlinear_xfm: Present only if VMHC is run- nonlinear warp transform from anatomical space to symmetric template space. Either ANTS or FSL-FNIRT warp depending on which was used.
  • anatomical_wm_mask: Binary mask of the white matter in anatomical space. This is a result of anatomical segmentation.
  • ants_affine_xfm: ANTS only- linear affine warp from anatomical space to template space.
  • ants_initial_xfm: ANTS only- “initial” linear warp from anatomical space to template space.
  • ants_rigid_xfm: ANTS only- rigid linear warp from anatomical space to template space.
  • ants_symmetric_affine_xfm: ANTS only- Same as above, but the warp to symmetric template space.
  • ants_symmetric_initial_xfm: ANTS only- Same as above, but the warp to symmetric template space.
  • ants_symmetric_rigid_xfm: ANTS only- Same as above, but the warp to symmetric template space.
  • centrality_outputs_smooth_zstd: Smoothed, z-score standardized centrality outputs (already in template space). Sub-directories in this folder for each type of centrality that was run (Degree, Eigenvector, LFCD).
  • dr_tempreg_maps_files_to_standard_smooth: Warped to standard template, smoothed Dual Regression outputs. Sub-directories in this folder for each map provided.
  • falff_to_standard_smooth_zstd: Warped to standard template, smoothed, z-score standardized output of f/ALFF.
  • frame_wise_displacement_jenkinson: 1-D file containing the vector of framewise displacement values between volumes, as calculated via Jenkinson.
  • frame_wise_displacement_power: 1-D file containing the vector of framewise displacement values between volumes, as calculated via Power.
  • functional_brain_mask: Binary mask of the brain in functional space.
  • functional_brain_mask_to_standard: Binary mask of the functional-space brain warped to standard template.
  • functional_freq_filtered: Preprocessed functional timeseries file all the way up to temporal filtering.
  • functional_nuisance_regressors: .mat file containing the data corresponding to each nuisance that was regressed out during nuisance regression.
  • functional_to_anat_linear_xfm: Functional-to-anatomical space linear transform. FSL-FLIRT format.
  • functional_to_standard: Preprocessed functional timeseries warped to standard template space.
  • mean_functional_to_standard: Mean functional (one-volume 3D file of functional scan) warped to standard template space.
  • mni_to_anatomical_nonlinear_xfm: Same as the anatomical_to_mni_nonlinear_xfm described above, except the inverse warp.
  • motion_correct: Motion-corrected functional timeseries in functional space, before the rest of functional preprocessing.
  • motion_params: Text file containing the single-value max or mean numbers of each head motion parameter/measure.
  • output_means: Text files containing the mean intensity values of each output or derivative. Used later in group-level analysis.
  • path_files_here: Text files containing full file paths to all of the C-PAC outputs in the output directory. Can be used for convenient file path parsing.
  • qc: PNG image files of all QC Interface montages, graphs, and charts. Can be easily viewed in one place in the QC-interface_{scan}_{nuisance/preprocessing strategy}.html files in the output directory (described below).
  • qc_files_here: Individual QC Interface HTML pages. Used later in the main QC Interface index generation.
  • reho_to_standard_smooth_zstd: Warped to standard template, smoothed, z-score standardized output of Regional Homogeneity (ReHo).
  • roi_timeseries_for_SCA: CSV files containing the extracted ROI timeseries for each ROI provided for Seed-Based Correlation Analysis (SCA).
  • roi_timeseries_for_SCA_multreg: Same as above, but the extracted ROI timeseries for each ROI provided for Multiple Regression (if different from SCA).
  • sca_roi_files: Raw correlation outputs of Seed-Based Correlation Analysis (SCA) for each ROI provided. Sub-directories in this folder for each ROI.
  • sca_roi_files_smooth: Smoothed version of the above.
  • sca_roi_files_to_standard: Warped to standard template version of sca_roi_files.
  • sca_roi_files_to_standard_fisher_zstd: Fisher r-to-z transformed version of sca_roi_files_to_standard.
  • sca_roi_files_to_standard_smooth: Smoothed version of sca_roi_files_to_standard.
  • sca_roi_files_to_standard_smooth_fisher_zstd: Fisher r-to-z transformed version of sca_roi_files_to_standard_smooth.
  • sca_tempreg_maps_files: Multiple Regression output files (already in template space).
  • sca_tempreg_maps_files_smooth: Smoothed version of sca_tempreg_maps_files.
  • sca_tempreg_maps_zstat_files: Z-stat file outputs of Multiple Regression. Produced by the –out_z option of FSL’s fsl_glm tool.
  • sca_tempreg_maps_zstat_files_smooth: Smoothed version of sca_tempreg_maps_zstat_files.
  • spatial_map_timeseries_for_DR: Text file containing the GLM output of the timeseries associated with the voxels in the spatial map provided to Spatial Regression. Used later in Temporal Regression to complete the Dual Regression derivative.
  • symmetric_anatomical_to_standard: Same as anatomical_to_standard, except warped to the symmetric anatomical template instead.
  • symmetric_mni_to_anatomical_nonlinear_xfm: Same as mni_to_anatomical_nonlinear_xfm, except the inverse warp from the symmetric template back to anatomical space.
  • vmhc_fisher_zstd_zstat_map: Fisher r-to-z transformed, Z-stat output of Voxel-Mirrored Homotopic Connectivity (VMHC).
  • voxel_timeseries: 1-D file (and also CSV and .npz files, if selected) containing the voxel-wise extracted timeseries based on each ROI provided. Sub-directories in this folder for each ROI.
  • QC-interface_{scan}_{nuisance/preprocessing strategy}.html: QC Interface HTML page for each scan and nuisance/preprocessing strategy combination.

Sub-Directory Descriptions

Each folder in the output directory may have a different amount of sub-directories, depending on how many functional scans specified in the data configuration, or how many pipeline customizations and forked strategies you specified in the pipeline configuration. For example, if there are multiple functional scans, you’ll see a folder for each one if you enter any of the functional-derived outputs’ folders, as seen below:

_images/output_dir_scans.png

An example of multiple sub-directories for multiple nuisance regression strategies:

_images/output_dir_strats.png

And sub-directories for each ROI provided for a derivative that may take in multiple ROIs from a mask or atlas- for example, Seed-Based Correlation Analysis (SCA) in this case:

_images/output_dir_masks.png

Full Output Directory Layout

The C-PAC output directory produced when “Extra Functional Outputs”, “Debugging Outputs”, and both Smoothed/Non-smoothed and both z-score standardized/raw outputs are all enabled, is considerably larger.

More detailed information coming soon.