Outputs of xcp_d
The xcp_d
outputs are written out in BIDS format and consist of three main parts.
Summary reports: There are two summary reports - an executive summary per session and a participant summary:
xcp_d/sub-${sub-id}_ses-${ses-id}_executive_summary.html xcp_d/sub-${sub-id}.html
Anatomical outputs: Anatomical outputs conists of anatomical preprocessed T1w/T2w and segmentation images in MNI spaces:
xcp_d/sub-${sub-id}/ses-${ses-id}/anat/sub-${sub-id}_ses-${ses-id}_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz xcp_d/sub-${sub-id}/ses-${ses-id}/anat/sub-${sub-id}_ses-${ses-id}_space-MNI152NLin6Asym_desc-preproc_dseg.nii.gz
If there are gifti files in fMRIPrep output, the gifti files are resmapled to standard sapce:
xcp_d/sub-${sub-id}/ses-${ses-id}/anat/sub-${sub-id}_ses-${ses-id}_den-32k_hemi-L_${surface}.surf.gii xcp_d/sub-${sub-id}/ses-${ses-id}/anat/sub-${sub-id}_ses-${ses-id}_den-32k_hemi-R_${surface}.surf.gii
Functional outputs: Functional outputs consist of processed/denoised BOLD data, timeseries, functional connectivity matrices, and resting-state derivatives.
Denoised or residual BOLD data:
# nifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-residual_bold.nii.gz xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-residual_bold.json # cifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_den-91k_desc-residual_bold.dtseries.nii xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_den-91k_desc-residual_bold.json
The json/sidecar contains paramters of the data and processing steps.
{ "Freq Band": [ 0.009, 0.08], "RepetitionTime": 2.0, "compression": true, "dummy vols": 0, "nuissance parameters": "27P", }
Functional timeseries and connectivity matrices:
#nifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_atlas-${atlasname}_desc-timeseries_bold.tsv xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_atlas-${atlasname}_desc-connectivity_bold.tsv #cifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_atlas-${atlasname}_den-91k_bold.pconn.nii xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_atlas-${atlasname}_den-91k_bold.ptseries.nii
Resting-state derivatives (ReHo and ALFF):
# nifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-reho_bold.nii.gz xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-alff_bold.nii.gz # cifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_den-32k_hemi-L_desc-reho_bold.func.gii xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_den-32k_hemi-R_desc-reho_bold.func.gii xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_den-91k_desc-alff_bold.dtseries.nii
Other outputs include quality control and framewise displacement:
# nifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-qc_bold.csv xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-framewisedisplacement_bold.tsv # cifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_desc-qc_bold.csv xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_space-fsLR_desc-framewisedisplacement_den-91k_bold.tsv
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-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_desc-framewisedisplacement_bold-DCAN.hdf5 # cifti xcp_d/sub-${sub-id}/ses-${ses-id}/func/sub-${sub-id}_ses-${ses-id}_task-${taskname}_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