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BEP 011: Structural derivatives #518
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# Structural (anatomical) derivatives | ||||||
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## Reconstructed cortical surfaces | ||||||
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Reconstructed cortical surfaces should be stored as GIFTI files, and each | ||||||
hemisphere should be stored separately. | ||||||
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Template: | ||||||
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```Text | ||||||
<pipeline_name>/ | ||||||
sub-<participant_label>/ | ||||||
anat/ | ||||||
<source_keywords>_hemi-{L|R}[_space-<surfspace>][_volspace-<volspace>][_desc-<label>]_<surftype>.surf.gii | ||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Do we need space and volspace? The surface file itself defines a surface space, so I suspect the interesting space here is "what volume is it embedded in". Can we think of use cases for either of I think we should also add the And looking ahead to BEM surfaces, the
Suggested change
Another approach could be to separate cortical surfaces from BEM surfaces, and keep |
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``` | ||||||
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Example: | ||||||
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```Text | ||||||
pipeline/ | ||||||
sub-001/ | ||||||
anat/ | ||||||
sub-001_hemi-L_pial.surf.gii | ||||||
sub-001_hemi-R_pial.surf.gii | ||||||
``` | ||||||
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The supported surface types (`<surftype>` suffix) are: | ||||||
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| `<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) | | ||||||
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Need to consider whether to add BEM here or in a separate section. |
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`space` filename keyword is restricted to | ||||||
[Surface Coordinate Spaces](../99-appendices/08-coordinate-systems.md#Surface) | ||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Currently there is no header for #Surface or #Volume to land on at ../99-appendices/08-coordinate-systems.md |
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and `volspace` corresponds to the 3D coordinate space described in | ||||||
[Volume Coordinate Spaces](../99-appendices/08-coordinate-systems.md#Volume). In | ||||||
contrast to other derivatives the sidecar metadata field `SpatialReference` (see | ||||||
[Introduction](01-introduction.md#Common-file-level-metadata-fields)) 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. | ||||||
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## Surface-Mapped Anatomical Scalar Derivatives | ||||||
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Surface-mapped scalar overlays should be stored as either GIFTI or CIFTI files | ||||||
(which allow for the combination of left and right hemispheres). | ||||||
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Template: | ||||||
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```Text | ||||||
<pipeline_name>/ | ||||||
sub-<participant_label>/ | ||||||
anat/ | ||||||
<source_keywords>[_hemi-{L|R}][_space-<space>][_desc-<label>]_<suffix>.{shape.gii|dscalar.nii} | ||||||
``` | ||||||
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The REQUIRED extension for scalar GIFTI files is `.shape.gii`. The `hemi` key is | ||||||
required for GIFTI files. For example: | ||||||
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```Text | ||||||
pipeline/ | ||||||
sub-001/ | ||||||
anat/ | ||||||
sub-001_hemi-L_curv.shape.gii | ||||||
sub-001_hemi-R_curv.shape.gii | ||||||
``` | ||||||
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The REQUIRED extension for scalar CIFTI files is `.dscalar.nii`. For example: | ||||||
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```Text | ||||||
pipeline/ | ||||||
sub-001/ | ||||||
anat/ | ||||||
sub-001_curv.dscalar.nii | ||||||
``` | ||||||
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The file `<suffix>` MUST be one of the following values: | ||||||
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| `<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 | | ||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I think we've discussed changing this to:
Suggested change
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. +1 on this, since |
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| `distortion` | Distortion map calculated from a surface registration | | ||||||
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## Morphometrics | ||||||
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Structural statistics produced by segmentation routines should be stored within | ||||||
tsv files, which could contain common parameters specified in the table below. | ||||||
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Template: | ||||||
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```Text | ||||||
<pipeline_name>/ | ||||||
sub-<participant_label>/ | ||||||
func|anat|dwi/ | ||||||
<source_keywords>[_desc-<label>]_morph.tsv | ||||||
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``` | ||||||
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Example: | ||||||
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```Text | ||||||
pipeline/ | ||||||
sub-001/ | ||||||
anat/ | ||||||
sub-001_desc-volumetric_morph.tsv | ||||||
``` | ||||||
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| 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 | | ||||||
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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: | ||||||
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```Text | ||||||
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 | ||||||
``` |
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I think we might want to generalize a little bit, as there isn't much leap from cortical surfaces to boundary-element-method (BEM) surfaces (see mri_make_bem_surfaces) like skull and skin that are not hemisphere-specific. The following text doesn't add those, but might pave the way.