This workflow performs all steps required to obtain the results from the Mindboggle enhanced volumetric tool from a T1 image input.
Mindboggle is an open-source tool for brain morphometry (tissue segmentation, cortical and subcortical parcellation and volumetry analysis). It takes in results from FreeSurfer and ANTs Morphology 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 neuro-anatomical substrates [Klein et al. 2017].
The workflow is fully automatic and includes the following steps:
- Image pre-processing including AC-PC alignment and optional de-facing (see Anatomy pre-processing)
- ANTs full volumetric pipeline (see ANTs Morphology 2.1.0)
- FreeSurfer pipeline (see FreeSurfer 5.3.0)
- Mindboggle tool (see Mindboggle 1.0)
Workflow scheme:
Mindboggle output examples
Corrected ANTs labels |
Corrected FreeSurfer labels |
Required inputs:
- T1: anatomical 3D image.
Isotropic resolution recommended
Must be labeled as 'T1' modality
Minimum input requirements:
- For optimal result reliability, isotropic resolution is recommended
- Recommended resolution: 1 mm isotropic.
- Minimum reliable resolution: 2mm isotropic.
Typical execution time:
- 8 hours
References:
Refer to the following tool pages for relevant references:
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