Outputs of xcp_d

The xcp_d outputs are written out in BIDS format and consist of three main parts.

1. 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
   

2. 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
   

3. Functional outputs: Functional outputs consist of processed/denoised BOLD data, timeseries, functional connectivity matrices, and resting-state derivatives.

   1. 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",
            }
      

   2. 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
      

   3. 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
      

   4. 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
      

   5. 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