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      Volumetric Report

      This tool derives whole brain volumetry and generates a report with a comparison of several structures to a database of normative controls.


      The volumetric quantities are calculated using the standard FreeSurfer Recon-all pipeline, with default configuration. This includes tissue segmentation on the T1 image and parcellation of grey matter areas according to the DKT40 atlas.
      The volumetric information from the various outputs of the FreeSurfer pipeline are extracted and includes in the database and the report.

      The normative database we use includes around 2300 healthy subjects from multiple public databases, indcuding ADHD 200, ABIDE, ADNI, The Nathan Kline Institute Rockland Sample, NACC, IXI and EDSD.

      The full workflow includes:

      • Full FreeSurfer recon all segmentation and cortical parcellation pipeline, outputing volumetry

      • The report generator extracts several structures from the FreeSurfer volumetry, calcuates percentiles from the normative database and produces report including volumetry and plots

      Required inputs:

      • T1: anatomical 3D image
        Isotropic resolution recommended, 1x1x1mm
        Must be labeled as 'T1' modality

      Minimum input requirements:

      • Image must contain the entire brain, cerebellum, intra-cranial cavity and the skull surrounding the brain
      • Image must be free of significant MRI imaging artefacts

      Output container files

      We explain the output files for each box. The modalities are shown in colored boxes and the tags are shown with outlined boxes. Each element represents a relevant file from the container, more might be present but they are not as important.

      DCM2NII

      • [T1] : T1 NIfTI file

      RECON ALL

      • [T1] / [HEAD] : T1 weighted image (not skull stripped)
      • [T1] / [BRAIN] : T1 weighted image (skull stripped)
      • [LABELS]: segmentation and parcellation label map
      • [TISSUE_SEGMENTATION]: Tissue segmentation
      • FREESURFER/: All FreeSurfer outputs, including volumes, surfaces and labels

      POST RECON ALL

      • [ASEG_STATS_1] : First segmentation stats file
      • [ASEG_STATS_2] : Second segmentation stats file
      • [REPORT] : PDF report of the box
      • [VOLUMETRIC] : Volumetry information in CSV format

      VOLUMETRIC REPORT GENERATOR

      • T1 / HEAD : T1 weighted image (not skull stripped)
      • CSV / ASEG_STATS : Segmentation statistics
      • CSV / CORTEX / VOLUME : Volumetric data of whole brain and sub-cortical regions 
      • CSV / CORTEX / THICKNESS : Thickness data of whole brain and sub-cortical regions 
      • CSV / LOBE / VOLUME : Volumetric data of brain lobes
      • CSV / LOBE / THICKNESS : Thickness data of brain lobes
      • CSV / VOLUMETRIC : Volumetric data of whole brain and sub-cortical regions 
      • LABELS : FreeSurfer segmentation and parcellation label map
      • REPORT : PDF report containing volumetric information
      • REPORT / SUMMARY : Summarised PDF report containing volumetric information
      • VOLUMETRIC / CSV : Table containing volumetric information for all brain regions 

      References

      Freesurfer recon-all: 

      [Dale et al. 1999]
      [Fischl et al. 1999]
      [Fischl et al. 2000]
      [Fischl et al. 2002]
      [Fischl et al. 2004]




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