Outputs of Connectome Mapper 3¶
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:
The five different brain parcellation are saved as:
scale5 corresponds to the parcellation scale.
Additionally, the description of parcel labels and the updated FreeSurfer color lookup table are saved as:
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/ ...
A FreeSurfer subjects directory is created in
freesurfer/ fsaverage/ mri/ surf/ ... sub-<subject_label>/ mri/ surf/ ... ...
fsaverage subject distributed with the running version of
FreeSurfer is copied into this directory.