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sf-pediatric

Outputs

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. The pipeline outputs results in a BIDS-like structure (BIDS derivatives are not officially described and accepted in the BIDS specification, so don’t hesitate to open an issue if something should be changed). As such, your root output folder will contain one folder per subject.

  • Directorysf-pediatric-v0.1.0/
    • dataset_description.json
    • Directorymultiqc/
      • …
    • participants.tsv
    • Directorysub-0001/
      • Directoryses-session/
        • Directoryanat/
          • …
        • Directorydwi/
          • …
        • Directoryfigures/
          • …
        • Directorymultiqc/
          • …
        • Directoryxfm/
          • …
      • Directoryses-session2/
        • …
    • Directorysub-0002/
      • Directoryses-session/
        • Directoryanat/
          • …
        • Directorydwi/
          • …
        • Directoryfigures/
          • …
        • Directorymultiqc/
          • …
        • Directoryxfm/
          • …
      • Directoryses-session2/
        • …
    • …

The pipeline will output only the final preprocessed files by default. This behavior is used to limit the number of files generated by the pipeline by omitting the publishing of intermediate results. It is particularly useful when running the pipeline on clusters where file quotas are often rapidly met. To opt-out from the lean output version (not recommended), set the --lean_output parameter to false when launching the pipeline (e.g., --lean_output false).

If you decided to run FreeSurfer (both recon-all or recon-all-clinical), FastSurfer, or M-CRIB-S as part of sf-pediatric, your output will be located (by default) alongside the sf-pediatric output folder. You can select the destination folder by using the --fs_output_dir parameter. If you do not specify and output folder destination, it will look like this:

  • Directorysf-pediatric-v0.1.0/
    • dataset_description.json
    • Directorymultiqc/
      • …
    • participants.tsv
    • Directorysub-0001/
      • …
    • Directorysub-0002/
      • …
    • …
  • Directoryfreesurfer/
    • Directorysub-0001/
      • …
    • Directorysub-0002/
      • …
    • …

Pipeline overview

Section titled “Pipeline overview”

The pipeline’s outputs are organized by subject and session in a BIDS-like structure. Below is a description of the output files organized by subfolder. If you used --lean_output false, you will find additional files than the ones described here (not recommended, this will highly increase the number of output files).

Output directories

Section titled “Output directories”
  • Root-level outputs - Population-level statistics and metadata
  • anat - Anatomical preprocessing, segmentation, and parcellation outputs
  • dwi - Diffusion preprocessing, local modeling, tractography, and connectivity outputs
  • figures - Quality control visualizations
  • xfm - Spatial transformations between image spaces
  • multiqc - Subject-level quality control reports. For a complete guide on how to navigate this report, please refer to this section.

Root-level outputs

Section titled “Root-level outputs”

The root output directory contains population-level files located alongside subject folders:

Output files
  • dataset_description.json: Dataset metadata following BIDS specification.
  • participants.tsv: Table containing subject and session information.
  • bundles_mean_stats.tsv: Population-level bundle statistics (mean values across bundles).
  • bundles_point_stats.tsv: Population-level bundle statistics (point-wise metrics).
  • cortical_{atlas}_area_{lh,rh}.tsv: Population-level cortical surface area statistics per hemisphere.
  • cortical_{atlas}_thickness_{lh,rh}.tsv: Population-level cortical thickness statistics per hemisphere.
  • cortical_{atlas}_volume_{lh,rh}.tsv: Population-level cortical volume statistics per hemisphere.
  • {atlas}_subcortical_volumes.tsv: Population-level subcortical volume statistics.
  • multiqc/: Folder containing population-wide MultiQC report. For

Subject-specific outputs

Section titled “Subject-specific outputs”

anat

Section titled “anat”

The anat/ folder contains all anatomical preprocessing outputs, tissue segmentation masks, parcellation labels, and cortical/subcortical statistics.

Output files

Preprocessed anatomical images

Section titled “Preprocessed anatomical images”
  • *_space-{T1w,T2w}_desc-preproc_T1w.nii.gz: Preprocessed T1w image in T1w or T2w space.
  • *_space-{T1w,T2w}_desc-preproc_T2w.nii.gz: Preprocessed T2w image in T1w or T2w space.
  • *_space-{T1w,T2w}_desc-brain_mask.nii.gz: Brain mask in T1w or T2w space.

Registered anatomical images in diffusion space

Section titled “Registered anatomical images in diffusion space”
  • *_space-DWI_desc-preproc_{T1w,T2w}.nii.gz: Preprocessed T1w/T2w image in diffusion space.

Registered anatomical images in template space

Section titled “Registered anatomical images in template space”
  • *_space-{template}_desc-preproc_{T1w,T2w}.nii.gz: Preprocessed T1w/T2w image in template space (e.g., MNIInfant).

Tissue segmentation

Section titled “Tissue segmentation”
  • *_space-DWI_label-{WM,GM,CSF}_mask.nii.gz: Binary tissue masks in diffusion space.
  • *_space-DWI_label-{WM,GM,CSF}_probseg.nii.gz: Tissue probability maps in diffusion space.
  • *_space-{template}_label-{WM,GM,CSF}_mask.nii.gz: Binary tissue masks in template space.
  • *_space-{template}_label-{WM,GM,CSF}_probseg.nii.gz: Tissue probability maps in template space.

Parcellation and segmentation

Section titled “Parcellation and segmentation”
  • *_seg-{atlas}_desc-labels_dseg.json: JSON file containing atlas label information.
  • *_seg-{atlas}_desc-labels_dseg.txt: Text file containing atlas label information.
  • *_seg-{atlas}_dseg.nii.gz: Atlas parcellation in native anatomical space.
  • *_seg-{atlas}_desc-dilated_dseg.nii.gz: Dilated atlas parcellation in native anatomical space.
  • *_space-DWI_seg-{atlas}_dseg.nii.gz: Atlas parcellation in diffusion space.
  • *_space-{template}_seg-{atlas}_dseg.nii.gz: Atlas parcellation in template space.

Cortical and subcortical statistics

Section titled “Cortical and subcortical statistics”
  • *_seg-{atlas}_hemi-{left,right}_stat-surfacearea.tsv: Cortical surface area per region.
  • *_seg-{atlas}_hemi-{left,right}_stat-thickness.tsv: Cortical thickness per region.
  • *_seg-{atlas}_hemi-{left,right}_stat-volume.tsv: Cortical volume per region.
  • *_seg-{atlas}_stat-subcortical.tsv: Subcortical structure volumes.

dwi

Section titled “dwi”

The dwi/ folder contains diffusion preprocessing outputs, local modeling results (DTI and fODF metrics), tractography outputs, bundles, and connectivity matrices.

Output files

Preprocessed diffusion images

Section titled “Preprocessed diffusion images”
  • *_desc-preproc_dwi.nii.gz: Preprocessed DWI image.
  • *_desc-preproc_dwi.bval: Final b-values file.
  • *_desc-preproc_dwi.bvec: Final corrected b-vectors file.
  • *_desc-preproc_b0.nii.gz: Mean B0 image.
  • *_desc-brain_mask.nii.gz: Brain mask in diffusion space.

Local modeling: DTI metrics

Section titled “Local modeling: DTI metrics”
  • *_model-tensor_param-fa_dwimap.nii.gz: Fractional Anisotropy (FA) map in native diffusion space.
  • *_model-tensor_param-md_dwimap.nii.gz: Mean Diffusivity (MD) map in native diffusion space.
  • *_model-tensor_param-ad_dwimap.nii.gz: Axial Diffusivity (AD) map in native diffusion space.
  • *_model-tensor_param-rd_dwimap.nii.gz: Radial Diffusivity (RD) map in native diffusion space.
  • *_model-tensor_param-mode_dwimap.nii.gz: Mode map in native diffusion space.
  • *_model-tensor_param-ga_dwimap.nii.gz: Geodesic Anisotropy (GA) map in native diffusion space.
  • *_model-tensor_param-rgb_dwimap.nii.gz: Color-coded directional FA map in native diffusion space.
  • *_model-tensor_param-diffusivity_dwimap.nii.gz: Tensor diffusivity in native diffusion space.
  • *_space-{template}_model-tensor_param-{fa,md,ad,rd,mode,ga,rgb}_dwimap.nii.gz: DTI metrics in template space.

Local modeling: fODF metrics

Section titled “Local modeling: fODF metrics”
  • *_model-csd_param-sh_dwimap.nii.gz: Fiber orientation distribution functions (fODF) in native diffusion space.
  • *_model-csd_param-peaks_dwimap.nii.gz: fODF peaks in native diffusion space.
  • *_model-csd_param-afdmax_dwimap.nii.gz: Maximum apparent fiber density (AFD) in native diffusion space.
  • *_model-csd_param-afdsum_dwimap.nii.gz: Sum of AFD across peaks in native diffusion space.
  • *_model-csd_param-afdtotal_dwimap.nii.gz: Total AFD in native diffusion space.
  • *_model-csd_param-nufo_dwimap.nii.gz: Number of fiber orientations (NuFO) in native diffusion space.
  • *_space-{template}_model-csd_param-{afdmax,afdsum,afdtotal,nufo}_dwimap.nii.gz: fODF-derived metrics in template space.
  • *_frf.txt: Fiber response function.

Tractography

Section titled “Tractography”
  • *_tract-wholebrain_track-sdstream_tractogram.trk: Whole-brain tractogram from the local tracking method in native diffusion space.
  • *_tract-wholebrain_track-pft_tractogram.trk: Whole-brain tractogram from the particle filter tracking (PFT) method in native diffusion space.
  • *_tract-wholebrain_track-sdstream_desc-ensemble_tractogram.trk: Whole-brain tractogram representing the concatenation of local and PFT methods in native diffusion space.
  • *_space-{template}_tract-wholebrain_track-sdstream_tractogram.trk: Whole-brain tractogram from local tracking in template space.
  • *_space-{template}_tract-wholebrain_track-pft_tractogram.trk: Whole-brain tractogram from PFT tracking in template space.
  • *_space-{template}_tract-wholebrain_track-sdstream_desc-ensemble_tractogram.trk: Whole-brain tractogram (ensemble) in template space.
  • *_space-DWI_label-seeding_desc-local_mask.nii.gz: Seeding mask for local tracking.
  • *_space-DWI_label-tracking_desc-local_mask.nii.gz: Tracking mask for local tracking.
  • *_space-DWI_label-seeding_desc-pft_mask.nii.gz: Seeding mask for PFT tracking.
  • *_space-DWI_label-exclude_desc-pft_probseg.nii.gz: Exclude probability map for PFT tracking.
  • *_space-DWI_label-include_desc-pft_probseg.nii.gz: Include probability map for PFT tracking.

Bundles (in bundles/ subdirectory)

Section titled “Bundles (in bundles/ subdirectory)”
  • *_tract-{bundleName}_hemi-{left,right}_track-sdstream_tractogram.trk: Individual bundle tractograms (cleaned, uniformized, and colored).

Tractometry statistics

Section titled “Tractometry statistics”
  • *_desc-mean_stats.tsv: Bundle-averaged metrics per subject.
  • *_desc-point_stats.tsv: Point-wise metrics along bundle profiles.

Connectivity analysis

Section titled “Connectivity analysis”
  • *_tract-wholebrain_seg-{atlas}_desc-filtered_tractogram.h5: Filtered whole-brain tractogram in native diffusion space.
  • *_tract-wholebrain_seg-{atlas}_desc-preproc_tractogram.h5: Preprocessed decomposed tractogram in native diffusion space.
  • *_space-{template}_tract-wholebrain_seg-{atlas}_desc-filtered_tractogram.h5: Filtered whole-brain tractogram in template space.
  • *_space-{template}_tract-wholebrain_seg-{atlas}_desc-preproc_tractogram.h5: Preprocessed decomposed tractogram in template space.
  • *_seg-{atlas}_stat-{metric}.npy: Connectivity matrices for various metrics (FA, MD, AD, RD, mode, streamline count, length, volume, AFD, NuFO, COMMIT weights, etc.).

figures

Section titled “figures”

The figures/ folder contains quality control visualizations generated during processing.

Output files
  • *_coverage_overlay_mqc.png: White matter coverage overlay on anatomical image.
  • *_gradients_mqc.png: Diffusion gradient sampling visualization.
  • *_labels_mqc.png: Parcellation labels overlay on anatomical image.
  • *_metrics_mqc.png: DTI metrics visualization.
  • *_tissue_segmentation_mqc.png: Tissue segmentation overlay.
  • *_seg-{atlas}_stat-{metric}_matrix.png: Connectivity matrix visualization for each metric.
  • *_seg-{atlas}_stat-{metric}_histogram.png: Histogram of connectivity values for each metric.

xfm

Section titled “xfm”

The xfm/ folder contains all spatial transformation files between different image spaces.

Output files

Between anatomical spaces

Section titled “Between anatomical spaces”
  • *_from-T1w_to-T2w_mode-image_desc-affine_xfm.mat: Affine transform from T1w to T2w space.
  • *_from-T2w_to-T1w_mode-image_desc-affine_xfm.mat: Affine transform from T2w to T1w space.

To diffusion space

Section titled “To diffusion space”
  • *_from-{T1w,T2w}_to-dwi_mode-image_desc-affine_xfm.mat: Affine transform from anatomical to diffusion space.
  • *_from-{T1w,T2w}_to-dwi_mode-image_desc-warp_xfm.nii.gz: Non-linear transform from anatomical to diffusion space.

From diffusion space

Section titled “From diffusion space”
  • *_from-dwi_to-{T1w,T2w}_mode-image_desc-warp_xfm.nii.gz: Non-linear transform from diffusion to anatomical space.

To template space

Section titled “To template space”
  • *_from-dwi_to-{template}_mode-image_desc-affine_xfm.mat: Affine transform from diffusion to template space.
  • *_from-dwi_to-{template}_mode-image_desc-warp_xfm.nii.gz: Non-linear transform from diffusion to template space.

From template space

Section titled “From template space”
  • *_from-{template}_to-dwi_mode-image_desc-affine_xfm.mat: Affine transform from template to diffusion space.
  • *_from-{template}_to-dwi_mode-image_desc-warp_xfm.nii.gz: Non-linear transform from template to diffusion space.

multiqc

Section titled “multiqc”

The multiqc/ folder contains subject-level HTML reports and associated data for quality control.

Output files
  • *_{timestamp}.html: Subject-level MultiQC HTML report.
  • *_{timestamp}_data/: Directory containing parsed statistics and raw data used in the report.
  • *_{timestamp}_plots/: Directory containing static plots in PDF, PNG, and SVG formats.

Subject-level reports display visual QC of key processing steps including sphere sampling, tissue segmentation, white matter coverage, label overlays, and metric maps.

MultiQC is a visualization tool that generates HTML reports on the subject-level and reports on population-level statistics. In your output folder, you will find a global MultiQC report (located next to your sub-XXXX folders). This is the population level report, containing statistics allowing the evaluation of outliers in terms of white matter coverage, number of streamlines, and volume, thickness, and surface area for each regions of the GM parcellation. For a complete guide on how to navigate these reports, please refer to the navigating the QC reports section.