Mindboggle 1.0

Mindboggle is an open-source pipeline for brain morphometry (tissue segmentation, cortical and subcortical parcellation and volumetry analysis). It takes in T1-weighted MRI data, makes use of the Freesurfer and ANTs morphometry tools and generates volume images and tabular information for further analysis. Mindboggle combines the morphology outputs of Freesurfer and ANTs and produces new labels which have been shown to more accurately reflect the real neuroanatomical substrates [Klein et al. 2017].

Mindboggle can be run as a stand-alone tool, requiring as inputs the outputs of previously computed Freesurfer and ANTs analysis on the platform on the same input dataset.
Alternatively, Mindboggle can be run as a full pipeline (choose the "Mindboggle pipeline" analysis tool), this tool only requires as input a T1 image and will perform all the required steps: pre-processing, Freesurfer, ANTs and Mindboggle. the Freesurfer and ANTs tools will be run in parallel, saving precious time.

Corrected Freesurfer labels

Corrected ANTs labels

Required inputs:

  • FreeSurfer: previously computed FreeSurfer analysis.
  • ANTs: previously computed ANTs morphology analysis. 
    Both input analysis must have been run on the same T1 image.

Minimum input requirements:

  • Outputs from ANTs and FreeSurfer must have the same image size and resolution, or analysis might fail
    In order to assure this the mindboggle pipeline may be used instead. 


  • Images:
    • tissueBrainExtractionBrain.nii.gz: preprocessed, skull-stripped and AC-PC aligned brain.

    • ants_labels_in_graywhite_hybrid_graywhite.nii.gz: hybrid segmentation filled with ANTs + FS cerebellar labels
    • freesurfer_wmparc_labels_in_hybrid_graywhite.nii.gz: hybrid segmentation filled with FS labels
  • Datasheets:
    • volume_per_ants_label.csv: volumetrics results per ANTs label

    • volume_per_freesurfer_label.csv: volumetrics results per FreeSurfer label

Typical execution time:

  • 1 hour


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