Outputs of Connectome Mapper 3

Note

Connectome Mapper 3 outputs are currently being updated to conform to the BIDS Common Derivatives specification (see BIDS Common Derivatives Extension).

Connectome Mapper Toolkit 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

Nipype Derivatives

A Nipype subjects directory is created in <bids_dataset/derivatives>/nipype, dedicated to all outputs generated by Nipype nodes relatively to their processing stage and pipeline type.

nipype/
    sub-<subject_label>/
        anatomical_pipeline/
            segmentation_stage/
                reconall/
                    _report/
                    command.txt
                    _inputs.pklz
                    _nodes.pklz
                    result_recon.pklz
                    <hash>.json
                mgz_convert/
                ...
            parcellation_stage/
            ...
        diffusion_pipeline/
        ...

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.