Understanding the Outputs
In this section, there is a description for all the output files provided at each processing stage. Important outputs from RABIES are stored into datasink/
folders, which will be generated in the output folder specified at execution.
Preprocessing Outputs
Multiple datasink folders are generated during preprocessing for different output types: anat_datasink/
, bold_datasink/
, unbiased_template_datasink/
, transforms_datasink/
and confounds_datasink/
.
anat_datasink/
: Includes the inhomogeneity-correction anatomical scans.anat_preproc/
: anatomical scans after inhomogeneity correction
bold_datasink/
: Includes all outputs related to the functional scans, where files are either resampled onto the native or commonspace of the EPI. The native space outputs are resampled over the anatomical scan from each corresponding MRI session, whereas the commonspace outputs are resampled over the reference atlas (the original EPI voxel resolution is unchanged during resampling unless specified otherwise in the RABIES command).native_bold/
: preprocessed EPI timeseries resampled to nativespacenative_brain_mask/
: brain mask in nativespacenative_WM_mask/
: WM mask in nativespacenative_CSF_mask/
: CSF mask in nativespacenative_labels/
: atlas labels in nativespacenative_bold_ref/
: a volumetric 3D EPI average generated from the 4Dnative_bold/
commonspace_bold/
: preprocessed EPI timeseries resampled to commonspacecommonspace_mask/
: brain mask in commonspacecommonspace_WM_mask/
: WM mask in commonspacecommonspace_CSF_mask/
: CSF mask in commonspacecommonspace_vascular_mask/
: vascular mask in commonspacecommonspace_labels/
: atlas labels in commonspacecommonspace_resampled_template/
: the commonspace anatomical template, resampled to the EPI’s dimensionsinput_bold/
: the raw EPI scans provided as inputs in the BIDS data folderinitial_bold_ref/
: the initial volumetric 3D EPI average generated from the 4Dinput_bold/
raw_brain_mask/
: brain mask resampled onto the 4Dinput_bold/
inho_cor_bold/
: the volumetric 3D EPI (initial_bold_ref/
) after inhomogeneity correction, which is later used for registration of the EPIinho_cor_bold_warped2anat/
: inho_cor_bold after co-registration to the associated anatomical image (anat_preproc/
)std_map_preprocess/
: the temporal standard deviation at each voxel on thecommonspace_bold/
tSNR_map_preprocess/
: the temporal signal-to-noise ratio (tSNR) of thecommonspace_bold/
unbiased_template_datasink/
: Outputs related to the generation of the unbiased template using https://github.com/CoBrALab/optimized_antsMultivariateTemplateConstruction. The unbiased template corresponds to the average of all anatomical (or functional with--bold_only
) scans after their alignment.unbiased_template/
: the unbiased template generated from the input dataset scanswarped_unbiased_template/
: the unbiased template, registered to the reference atlas in commonspace
transforms_datasink/
: datasink for all the relevant transform files resampling between the different spaces. The bold_to_anat registration transformed the raw EPI to overlap with the anatomical image, correcting for susceptibility distortions, which corresponds to the native space. The native_to_unbiased registration overlaps every scans to the generated unbiased template, and then the unbiased_to_atlas corresponds to the registration of the unbiased template with the reference atlas, which defines the commonspace.bold_to_anat_affine/
: affine transforms from the EPI co-registration to the anatomical imagebold_to_anat_warp/
: non-linear transforms from the EPI co-registration to the anatomical imagebold_to_anat_inverse_warp/
: inverse of the non-linear transforms from the EPI co-registration to the anatomical imagenative_to_unbiased_affine/
: affine transforms for the alignment between native space and the unbiased templatenative_to_unbiased_warp/
: non-linear transforms for the alignment between native space and the unbiased templatenative_to_unbiased_inverse_warp/
: inverse of the non-linear transforms for the alignment between native space and the unbiased templateunbiased_to_atlas_affine/
: affine transforms for the alignment between unbiased template and the atlas in commonspaceunbiased_to_atlas_warp/
: non-linear transforms for the alignment between unbiased template and the atlas in commonspaceunbiased_to_atlas_inverse_warp/
: inverse of the non-linear transforms for the alignment between unbiased template and the atlas in commonspace
motion_datasink/
: files derivated from motion estimationmotion_params_csv/
: contains the 24 motion parameters which can be used as nuisance regressors at the confound correction pipeline stage.FD_csv/
: a CSV file with timescourses for either the mean or maximal framewise displacement (FD) estimations.FD_voxelwise/
: a Nifti image which contains framewise displacement evaluated at each voxelpos_voxelwise/
: a Nifti image which tracks the displacement (derived from the head motion realignment parameters) of each voxel across time
Confound Correction Outputs
Important outputs from confound correction will be found in the confound_correction_datasink/
:
confound_correction_datasink/
:cleaned_timeseries/
: cleaned timeseries after the application of confound correctionframe_censoring_mask/
: contains CSV files each recording as a boolean vector which timepoints were censored if frame censoring was applied.aroma_out/
: if--ica_aroma
is applied, this folder contains outputs from running ICA-AROMA, which includes the MELODIC ICA outputs and the component classification resultsplot_CR_overfit/
: will contain figures illustrating the variance explained by random regressors during confound correction, and the variance explained by the real regressors after substrating the variance from random regressors.background_masking_fig/
: will illustrate the image background masks automatically generated if using--image_scaling background_noise
Analysis Outputs
Outputs from analyses will be found in the analysis_datasink/
, whereas outputs relevant to the --data_diagnosis
are found in data_diagnosis_datasink/
:
analysis_datasink/
:group_ICA_dir/
: complete output from MELODIC ICA, which the melodic_IC.nii.gz Nifti which gives all spatial components, andreport/
folder which includes a HTML visualization.matrix_data_file/
: .pkl file which contains a 2D numpy array representing the whole-brain correlation matrix. If--ROI_type parcellated
is selected, the row/column indices of the array are matched in increasing order of the atlas ROI label number.matrix_fig/
: .png file which displays the correlation matrixseed_correlation_maps/
: nifti files for seed-based connectivity analysis, where each seed provided in--seed_list
has an associated voxelwise correlation mapsdual_regression_nii/
: the spatial maps from dual regression, which correspond to the linear coefficients from the second regression. The list of 3D spatial maps obtained are concatenated into a 4D Nifti file, where the order of component is consistent with the priors provided in--prior_maps
.dual_regression_timecourse_csv/
: a CSV file which stores the outputs from the first linear regression during dual regression. This corresponds to a timecourse associated to each prior component from--prior_maps
.NPR_prior_filename/
: spatial components fitted during NPRNPR_prior_timecourse_csv/
: timecourses associated to each components from NPR_prior_filenameNPR_extra_filename/
: the extra spatial components fitted during NPR which were not part of priorsNPR_extra_timecourse_csv/
: timecourses associated to each components from NPR_extra_filename
data_diagnosis_datasink/
:figure_temporal_diagnosis/
: figure which displays scan-level temporal features from the spatiotemporal diagnosisfigure_spatial_diagnosis/
: figure which displays scan-level spatial features from the spatiotemporal diagnosisanalysis_QC/
: group-level features of data quality from--data_diagnosis
sample_distributions/
: contains the distribution plots{analysis}_sample_distribution.png
: the distribution plot for a given network analysis{analysis}_outlier_detection.csv
: a CSV which associates the measures displayed in the distribution plot with corresponding scan IDs
parametric_stats/
: group statistical report for analysis quality control (using parametric measures)DR{component #}_QC_maps.png
: The _QC_maps.png files are displaying statistical maps relevant to analysis quality control. The DR refers to dual regression analysis, and the {component #} is relating the file to one of the BOLD components specified in--prior_bold_idx
DR{component #}_QC_stats.csv
: a follow-up to _QC_maps.png which allows for the quantitative categorization of data quality outcomes in Desrosiers-Gregoire et al. (in prep.)seed_FC{seed #}_QC_maps.png
: same statistical maps as withDR{component #}_QC_maps.png
, but for seed-based connectivity analysisseed_FC{seed #}_QC_stats.csv
: same measures as withDR{component #}_QC_maps.png
, but for seed-based connectivity analysis
non_parametric_stats/
: same asparametric_stats/
, but using non-parametric measures
temporal_info_csv/
: CSV file containing the data plotted withfigure_temporal_diagnosis/
spatial_VE_nii/
: Nifti file with the confound regression percentage variance explained (R^2) at each voxelCR_prediction_std_nii/
: Nifti file with the confound regression variance explained at each voxelrandom_CR_std_nii/
: Nifti file with the variance explained from random regressors at each voxelcorrected_CR_std_nii/
: Nifti file with the confound regression variance explained at each voxel after removing the variance explained by random regressorstemporal_std_nii/
: the standard deviation at each voxel after confound correctionGS_cov_nii/
: the covariance of each voxel with the global signal