FIRST is a model-based segmentation/registration tool for subcortical gray matter structures. The shape/appearance models used in FIRST are constructed from manually segmented images provided by the Center for Morphometric Analysis (CMA), MGH, Boston. The manual labels are parameterized as surface meshes and modeled as a point distribution model. Deformable surfaces are used to automatically parameterize the volumetric labels in terms of meshes; the deformable surfaces are constrained to preserve vertex correspondence across the training data. Furthermore, normalized intensities along the surface normals are sampled and modeled. The shape and appearance model is based on multivariate Gaussian assumptions.

The full Workflow includes

  • DICOM to NIfTI file conversion
  • FIRST Tool

Required inputs

  • T1: Anatomical 3D image
    • 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.

Output files

  • Report: Structured report in pdf format including the most relevant results of the analysis.
  • quantification.csv: Comma-separated values file containing the volumes of the segmented structures.
  • T1: Original image in NIfTI format.
  • out_all_fast_firstseg.nii.gz : NIfTI mask containing the segmented labels.
  • FIRST files: All the output files from FIRST.


Typical execution time

  • 40 minutes


  • Structures to segment: The user can select which structures to be segmented from the 15 that are available.
  • Boundary Correction Method: automatic by default, will use the best method for every scenario.
  • Skull Stripped Data: This option needs to be checked if the input data was previously skull stripped.



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