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Structural (anatomical) derivatives

Reconstructed cortical surfaces

Reconstructed cortical surfaces should be stored as GIFTI files, and each hemisphere should be stored separately.

Template:

<pipeline_name>/
    sub-<label>/
        anat/
            <source-entities>_hemi-{L|R}[_space-<label>][_den-<label>][_desc-<label>]_<surftype>.surf.gii

Example:

└─ pipeline/
   └─ sub-001/
      └─ anat/
         ├─ sub-001_hemi-L_pial.surf.gii 
         └─ sub-001_hemi-R_pial.surf.gii

The supported surface types (<surftype> suffix) are:

Name suffix Description
Flattened surface flat The flattened surface (used for visualization).
Inflated surface inflated An inflation of the midthickness surface (useful for visualization).
Midpoints between white matter and pial matter midthickness The midpoints between white matter and pial surfaces.
Gray matter / pial matter border pial The gray matter / pial matter border.
Smoothed gray matter / white matter border smoothwm The smoothed gray matter / white matter border.
Sphere sphere The sphere (used for registration - see transforms for nomenclature)
Very-inflated surface vinflated A very-inflated midthickness surface (also for visualization).
Gray matter / white matter border for the cortex white The gray matter / white matter border for the cortex.

  • space-<label> is REQUIRED to disambiguate derivatives defined with respect to different coordinate systems, following the general BIDS-Derivatives specifications.

  • den-<label> is REQUIRED to disambiguate different surface sampling densities.

Surface-Mapped Anatomical Scalar Derivatives

Surface-mapped scalar overlays should be stored as either GIFTI or CIFTI files (which allow for the combination of left and right hemispheres).

Template:

<pipeline_name>/
    sub-<label>/
        anat/
            <source-entities>[_hemi-{L|R}][_space-<label>][_den-<label>][_desc-<label>]_<suffix>.{shape.gii|dscalar.nii}

The REQUIRED extension for scalar GIFTI files is .shape.gii. The hemi key is required for GIFTI files. For example:

└─ pipeline/
   └─ sub-001/
      └─ anat/
         ├─ sub-001_hemi-L_curv.shape.gii 
         └─ sub-001_hemi-R_curv.shape.gii

The REQUIRED extension for scalar CIFTI files is .dscalar.nii. For example:

└─ pipeline/
   └─ sub-001/
      └─ anat/
         └─ sub-001_curv.dscalar.nii

The file <suffix> MUST be one of the following values:

Name suffix Description
T1w to T2w ratio, a proxy for myelination T1wT2wratio T1w to T2w ratio, a proxy for myelination.
Discretized surface area across regions area Discretized surface area across regions.
Cortical surface curvature indices curv Cortical surface curvature indices.
Marked regions with surface defects defects Marked regions with surface defects.
Distance from a point dist Distance from a point.
Distortion map calculated from a surface registration distortion Distortion map calculated from a surface registration.
Sulcal depth sulc Sulcal depth.
Cortical thickness thickness Cortical thickness.

Morphometrics

Structural statistics produced by segmentation routines should be stored within tsv files, which could contain common parameters specified in the table below.

Template:

<pipeline_name>/
    sub-<label>/
        func|anat|dwi/
            <source-entities>[_desc-<label>]_morph.tsv

Example:

└─ pipeline/
   └─ sub-001/
      └─ anat/
         └─ sub-001_desc-volumetric_morph.tsv
Column name Requirement Level Data type Description
index REQUIRED integer The label integer index.

Values in index MUST be unique.
name REQUIRED string The unique structure name.
centroid OPTIONAL array of numbers Center coordinate of the structure.
volume OPTIONAL number Volume of the structure.
intensity OPTIONAL number Intensity of the voxels within the structure.
thickness OPTIONAL number Thickness of the cortical structure.
area OPTIONAL number Surface area of the cortical structure.
curv OPTIONAL number Curvature index of the cortical structure.
Additional Columns OPTIONAL n/a Additional columns are allowed if they are defined in the associated metadata file.

Some parameters might require unit specification or have multiple associated statistics (such as avg, std, min, max, range). The suggested syntax for such columns is <parameter>[-<stat>][-<units>]. An example volumetric stats file might look something like this:

index  name               volume-mm3  intensity-avg  intensity-std
11     Brainstem          23415.9     80.11          3.40
32     Left-Hippocampus   5349.7      75.23          2.27
32     Right-Hippocampus  4112.1      76.98          4.01