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 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, "nuissance 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 and framewise displacement:
# 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 # 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
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. 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