Outputs of xcp_d
The xcp_d
outputs are written out in BIDS format and consist of three main parts.
A note on BIDS compliance
xcp_d
attempts to follow the BIDS specification as best as possible.
However, many xcp_d
derivatives are not currently covered by the specification.
In those instances, we attempt to follow recommendations from existing BIDS Extension Proposals (BEPs),
which are in-progress proposals to add new features to BIDS.
Three BEPs that are of particular use in xcp_d
are
BEP012: Functional preprocessing derivatives,
BEP017: BIDS connectivity matrix data schema,
and
BEPXXX: Atlas Specification
(currently unnumbered).
In cases where a derivative type is not covered by an existing BEP, we have simply attempted to follow the general principles of BIDS.
If you discover a problem with the BIDS compliance of xcp_d
’s derivatives, please open an issue in the xcp_d
repository.
Summary reports: There are two summary reports - an executive summary per session (if
--dcan-qc
is used) and a participant summary:xcp_d/sub-<label>[_ses-<label>]_executive_summary.html xcp_d/sub-<label>.html
Anatomical outputs: Anatomical outputs consist of anatomical preprocessed T1w/T2w and segmentation images in MNI spaces:
xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-MNI152NLin6Asym_dseg.nii.gz
If the
--warp-surfaces-native2std
option is selected, and reconstructed surfaces are available in the preprocessed dataset, then these surfaces will be warped to fsLR space at 32k density:xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_midthickness.surf.gii xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_inflated.surf.gii xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_vinflated.surf.gii xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-fsLR_den-32k_hemi-<L|R>_midthickness.surf.gii xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-fsLR_den-32k_hemi-<L|R>_pial.surf.gii xcp_d/sub-<label>/[ses-<label>/]anat/<source_entities>_space-fsLR_den-32k_hemi-<L|R>_smoothwm.surf.gii
Functional outputs: Functional outputs consist of processed/denoised BOLD data, timeseries, functional connectivity matrices, and resting-state derivatives.
Denoised or residual BOLD data:
# Nifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_desc-denoised_bold.nii.gz xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_desc-denoised_bold.json # Cifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_den-91k_desc-denoised_bold.json
The json/sidecar contains parameters of the data and processing steps.
{ "Freq Band": [ 0.009, 0.08], "RepetitionTime": 2.0, "compression": true, "dummy vols": 0, "nuisance parameters": "27P", }
Functional timeseries and connectivity matrices:
#Nifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_atlas-<label>_timeseries.tsv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_atlas-<label>_measure-pearsoncorrelation_conmat.tsv #Cifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_atlas-<label>_den-91k_timeseries.ptseries.nii xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_atlas-<label>_den-91k_measure-pearsoncorrelation_conmat.pconn.nii
Resting-state derivatives (Regional Homogeneity and ALFF):
# Nifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_reho.nii.gz xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_alff.nii.gz xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_desc-smooth_alff.nii.gz # Cifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_den-91k_reho.dscalar.nii xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_den-91k_alff.dscalar.nii xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_den-91k_desc-smooth_alff.dscalar.nii
Important
The smoothed ALFF image will only be generated is smoothing is enabled (e.g., with the
--smoothing parameter
).Important
ALFF images will not be generated if bandpass filtering is disabled (e.g., with the
--disable-bandpass-filtering
parameter).Other outputs include quality control, framewise displacement, and confounds files:
# Nifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_qc.csv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>[_desc-filtered]_motion.tsv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_outliers.tsv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_design.tsv # Cifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_qc.csv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>[_desc-filtered]_motion.tsv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_outliers.tsv xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_design.tsv
The
[desc-filtered]_motion.tsv
is a tab-delimited file with seven columns; one for each of the six filtered motion parameters, as well as “framewise_displacement”. If no motion filtering was applied, this file will not have thedesc-filtered
entity.DCAN style scrubbing file (if
--dcan-qc
is used). This file is in hdf5 format (readable by h5py), and contains binary scrubbing masks from 0.0 to 1mm FD in 0.01 steps. At each step the following variables are present:# Nifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-<label>_desc-framewisedisplacement_bold-DCAN.hdf5 # Cifti xcp_d/sub-<label>/[ses-<label>/]func/<source_entities>_space-fsLR_desc-framewisedisplacement-bold-DCAN.hdf5 These files have the following keys: 1. FD_threshold: a number >= 0 that represents the FD threshold used to calculate the metrics in this list 2. frame_removal: a binary vector/array the same length as the number of frames in the concatenated time series, indicates whether a frame is removed (1) or not (0) 3. format_string (legacy): a string that denotes how the frames were excluded -- uses a notation devised by Avi Snyder 4. total_frame_count: a whole number that represents the total number of frames in the concatenated series 5. remaining_frame_count: a whole number that represents the number of remaining frames in the concatenated series 6. remaining_seconds: a whole number that represents the amount of time remaining after thresholding 7. remaining_frame_mean_FD: a number >= 0 that represents the mean FD of the remaining frames