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-<participant_label>/
        anat/
            <source_keywords>_hemi-{L|R}[_space-<surfspace>][_volspace-<volspace>][_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:

<surftype> Description
wm The gray matter / white matter border for the cortex
smoothwm The smoothed gray matter / white matter border
pial The gray matter / pial matter border
midthickness The midpoints between wm and pial surfaces
inflated An inflation of the midthickness surface (useful for visualization)
vinflated A very-inflated midthicknesss surface (also for visualization)
sphere The sphere (used for registration - see transforms for nomenclature)
flat The flattened surface (used for visualization)

space filename keyword is restricted to Surface Coordinate Spaces and volspace corresponds to the 3D coordinate space described in Volume Coordinate Spaces. In contrast to other derivatives the sidecar metadata field SpatialReference (see Introduction) is not required for any space, but is recommended when volspace is set to individual. In such case it should point to the volume defining the 3D coordinate system with witch the surface mesh is aligned with.

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-<participant_label>/
        anat/
            <source_keywords>[_hemi-{L|R}][_space-<space>][_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:

<suffix> Description
curv Cortical surface curvature indices
thickness Cortical thickness
area Discretized surface area across regions
dist Distance from a point
defects Marked regions with surface defects
sulc Sulcal depth
myelinmap Myelin map calculated from T1w to T2w ratio
distortion Distortion map calculated from a surface registration

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-<participant_label>/
        func|anat|dwi/
            <source_keywords>[_desc-<label>]_morph.tsv

Example:

pipeline/
    sub-001/
        anat/
            sub-001_desc-volumetric_morph.tsv
Column name Description
index RECOMMENDED. Label integer index
name RECOMMENDED. Structure name
centroid OPTIONAL. Center coordinate of structure
volume OPTIONAL. Volume of structure
intensity OPTIONAL. Intensity of voxels within structure
thickness OPTIONAL. Thickness of cortical structure
area OPTIONAL. Surface area of cortical structure
curv OPTIONAL. Curvature index of cortical structure

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