Outputs of Multi-Scale Brain Parcellator

Note

Multi-Scale Brain Parcellator outputs are currently being updated to conform to the BIDS Common Derivatives specification (see BIDS Common Derivatives Extension).

Multi-Scale Brain Parcellator Derivatives

Processed, or derivative, data are written to <bids_dataset/derivatives>/cmp/sub-<subject_label>/. In this folder, a configuration file generated and used for processing each participant is saved as sub-<subject_label>_anatomical_config.ini. It summarizes pipeline workflow options and parameters used for processing.

Anatomical derivatives in the original T1w space are placed in each subject’s anat subfolder including:

  • anat/sub-<subject_label>_desc-head_T1w.nii.gz
  • anat/sub-<subject_label>_desc-brain_T1w.nii.gz
  • anat/sub-<subject_label>_desc-brain_mask.nii.gz
  • anat/sub-<subject_label>_label-WM_dseg.nii.gz
  • anat/sub-<subject_label>_label-GM_dseg.nii.gz
  • anat/sub-<subject_label>_label-CSF_dseg.nii.gz

The five different brain parcellation are saved as:

  • anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas.nii.gz

where <scale_label> : scale1, scale2, scale3, scale4, scale5 corresponds to the parcellation scale.

Additionally, the description of parcel labels and the updated FreeSurfer color lookup table are saved as:

  • anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas.graphml
  • anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas_FreeSurferColorLUT.txt

Finally, parcel volumetry results for each scale are saved in a TSV file as:

  • anat/sub-<subject_label>_label-L2018_desc-<scale_label>_stats.tsv

FreeSurfer Derivatives

A FreeSurfer subjects directory is created in <bids_dataset/derivatives>/freesurfer.

freesurfer/
    fsaverage/
        mri/
        surf/
        ...
    sub-<subject_label>/
        mri/
        surf/
        ...
    ...

The fsaverage subject distributed with the running version of FreeSurfer is copied into this directory.