{
  "template": "MNI ICBM152 nonlinear symmetric 2009c",
  "space": "RAS mm",
  "source": "Juan Eugenio Iglesias, FreeSurfer brainstem atlas-prior export, source page modified 2025-03-03",
  "source_url": "https://surfer.nmr.mgh.harvard.edu/fswiki/SubfieldAtlasesICBMspace",
  "method_url": "https://doi.org/10.1016/j.neuroimage.2015.02.065",
  "inputs": [
    {
      "url": "https://surfer.nmr.mgh.harvard.edu/fswiki/SubfieldAtlasesICBMspace?action=AttachFile&do=get&target=Brainstem.zip",
      "file": "Brainstem.zip",
      "sha256": "f6ad672136102669955ee803f27c188a5e172a326a61fb9818d12fb4707fe5c2",
      "bytes": 321552,
      "entries": [
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        "BrainstemProbs.MNIsymSpace.names.txt"
      ]
    },
    {
      "url": "https://surfer.nmr.mgh.harvard.edu/fswiki/SubfieldAtlasesICBMspace?action=AttachFile&do=get&target=mni_icbm152_nlin_sym_09c_nifti.zip",
      "file": "mni_icbm152_nlin_sym_09c_nifti.zip",
      "sha256": "ed981b4611ddd797a22f539035979723ecb1badebd06dcd85df149b5ef00890d",
      "bytes": 57583823,
      "entries": [
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        "mni_icbm152_nlin_sym_09c/mni_icbm152_gm_tal_nlin_sym_09c.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_csf_tal_nlin_sym_09c.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_t2_tal_nlin_sym_09c.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_wm_tal_nlin_sym_09c.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_t1_tal_nlin_sym_09c.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_t1_tal_nlin_sym_09c_mask.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_t1_tal_nlin_sym_09c_face_mask.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_t1_tal_nlin_sym_09c_eye_mask.nii",
        "mni_icbm152_nlin_sym_09c/mni_icbm152_pd_tal_nlin_sym_09c.nii",
        "COPYING"
      ]
    }
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    [
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    [
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  "MRI_affine": [
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    [
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  "processing": "Native-space, background-inclusive argmax after clipping numerical roundoff and normalizing probabilities. Binary masks, Lewiner marching cubes at 0.5 with 1-voxel zero padding; six SCP ambiguous-cell tessellation vertices are cell centers, not exact isolevel samples; remove only planar cap triangles at cropped inferior z=-78.5 mm. No smoothing, decimation, fsaverage registration, or assignment of nuclei/tracts.",
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    "window": [
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    "interpolation": "linear MRI sampling; WebP quality 90",
    "outside_image": "black, not anatomical absence"
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  "coverage": [
    {
      "label": 173,
      "assigned_voxels": 9522,
      "vertices": 4390,
      "triangles": 8772,
      "boundary_edges": 0,
      "removed_crop_cap_triangles": 0,
      "nonmanifold_edges": 0
    },
    {
      "label": 174,
      "assigned_voxels": 20725,
      "vertices": 6550,
      "triangles": 13096,
      "boundary_edges": 0,
      "removed_crop_cap_triangles": 0,
      "nonmanifold_edges": 0
    },
    {
      "label": 175,
      "assigned_voxels": 7110,
      "vertices": 3395,
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      "boundary_edges": 22,
      "removed_crop_cap_triangles": 66,
      "nonmanifold_edges": 0
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    {
      "label": 178,
      "assigned_voxels": 426,
      "vertices": 842,
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      "boundary_edges": 0,
      "removed_crop_cap_triangles": 0,
      "nonmanifold_edges": 0
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  ],
  "limitations": [
    "Source probabilities lie approximately in MNI space, not individual histology or a newly run segmentation.",
    "Medulla reaches the inferior source boundary; open edge denotes truncation.",
    "Labels are not split into left/right objects. SCP is one source label covering its mapped components.",
    "This study uses a different template from other atlas modes. No fsaverage surface is overlaid.",
    "The four labels do not expose internal nuclei or all fibers."
  ],
  "licenses": [
    "../FREESURFER-LICENSE.txt",
    "MNI-LICENSE.txt"
  ],
  "review": "Internal source/grid/topology checks; qualified anatomical review pending"
}