{
  "id": "2006.15460",
  "version": "v1",
  "published": "2020-06-27T22:21:23.000Z",
  "updated": "2020-06-27T22:21:23.000Z",
  "title": "Fast automatic segmentation of thalamic nuclei from MP2RAGE acquisition at 7 Tesla",
  "authors": [
    "Ritobrato Datta",
    "Micky K. Bacchus",
    "Dushyant Kumar",
    "Mark A. Elliott",
    "Aditya Rao",
    "Sudipto Dolui",
    "Ravinder Reddy",
    "Brenda L Banwell",
    "Manojkumar Saranathan"
  ],
  "comment": "13 pages, 4 figures",
  "categories": [
    "eess.IV",
    "q-bio.QM"
  ],
  "abstract": "Purpose: Thalamic nuclei are largely invisible in conventional MRI due to poor contrast. Thalamus Optimized Multi-Atlas Segmentation (THOMAS) provides automatic segmentation of 12 thalamic nuclei using white-matter-nulled (WMn) MPRAGE sequence at 7T. Application of THOMAS to Magnetization Prepared 2 Rapid Gradient Echo (MP2RAGE) sequence acquired at 7T has been investigated in this study. Methods: 8 healthy volunteers and 5 pediatric-onset multiple sclerosis patients were recruited at the Children's Hospital of Philadelphia and scanned at Siemens 7T with WMn-MPRAGE and multi-echo MP2RAGE (ME-MP2RAGE) sequences. White-matter-nulled contrast was synthesized (MP2-SYN) from T1 maps from ME-MP2RAGE sequence. Thalamic nuclei were segmented using THOMAS joint label fusion algorithm from WMn-MPRAGE and MP2-SYN datasets. THOMAS pipeline was modified to use majority voting to segment the bias corrected MP2-UNI images. Thalamic nuclei from MP2-SYN and MP2-UNI images were evaluated against corresponding nuclei obtained from WMn-MPRAGE images using dice coefficients, volume similarity indices (VSI) and distance between centroids. Results: For MP2-SYN, dice > 0.85 and VSI > 0.95 was achieved for the 5 larger nuclei and dice > 0.6 and VSI > 0.7 was achieved for the 7 smaller nuclei. The dice and VSI were slightly higher whilst the distance between centroids were smaller for MP2-SYN compared to MP2-UNI, indicating improved performance using the synthesized WMn image. Discussion: THOMAS algorithm can successfully segment thalamic nuclei in routinely acquired bias-free MP2RAGE images with essentially equivalent quality when evaluated against WMn-MPRAGE, hence has wider applicability in studies focused on thalamic involvement in aging and disease.",
  "revisions": [
    {
      "version": "v1",
      "updated": "2020-06-27T22:21:23.000Z"
    }
  ],
  "analyses": {
    "keywords": [
      "thalamic nuclei",
      "fast automatic segmentation",
      "mp2rage acquisition",
      "acquired bias-free mp2rage images",
      "thomas joint label fusion algorithm"
    ],
    "note": {
      "typesetting": "TeX",
      "pages": 13,
      "language": "en",
      "license": "arXiv",
      "status": "editable"
    }
  }
}