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BEP 011: Structural derivatives #518

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effigies
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@effigies effigies commented Jun 30, 2020

As a follow-up to #265 (Common Derivatives), this PR adds structural derivatives. This was taken directly from the draft PR #207.

I have not made any modifications to bring it into line with the final common derivatives yet, but I wanted to get this started.

I will go through and comment up issues I see so we can discuss a bit before I push through with them.

cc @edickie @vsiless

@effigies effigies requested a review from edickie as a code owner Jun 30, 2020
## Reconstructed cortical surfaces

Reconstructed cortical surfaces should be stored as GIFTI files, and each
hemisphere should be stored separately.
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@effigies effigies Jun 30, 2020

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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.

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## Reconstructed cortical surfaces
Reconstructed cortical surfaces should be stored as GIFTI files, and each
hemisphere should be stored separately.
## Reconstructed surfaces
A surface is defined by three-dimensional vertex coordinates, and a set of triangles,
or triplets of indices into the coordinate array.
Surfaces MUST be stored as [GIFTI] surface files, with one surface per file.
For structures with hemispheres, the `hemi-` entity SHOULD be used to distinguish the
surface files corresponding to each hemisphere.
For example, reconstructions of the cortical sheet are typically split into two disjoing
surfaces.

<pipeline_name>/
sub-<participant_label>/
anat/
<source_keywords>_hemi-{L|R}[_space-<surfspace>][_volspace-<volspace>][_desc-<label>]_<surftype>.surf.gii
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@effigies effigies Jun 30, 2020

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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 space or volspace?

I think we should also add the den-<label> entity. As a (probably wrong) proposal, this might obviate the need for surface space.

And looking ahead to BEM surfaces, the hemi- might be considered RECOMMENDED not REQUIRED.

Suggested change
<source_keywords>_hemi-{L|R}[_space-<surfspace>][_volspace-<volspace>][_desc-<label>]_<surftype>.surf.gii
<source_entities>[_hemi-{L|R}][_den-<label>][_desc-<label>]_<suffix>.surf.gii

Another approach could be to separate cortical surfaces from BEM surfaces, and keep hemi REQUIRED here.

| `<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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@effigies effigies Jun 30, 2020

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Need to consider whether to add BEM here or in a separate section.

| `dist` | Distance from a point |
| `defects` | Marked regions with surface defects |
| `sulc` | Sulcal depth |
| `myelinmap` | Myelin map calculated from T1w to T2w ratio |
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@effigies effigies Jun 30, 2020

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I think we've discussed changing this to:

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| `myelinmap` | Myelin map calculated from T1w to T2w ratio |
| `T1wT2wratio`| T1w to T2w ratio, a proxy for myelination |

@sappelhoff sappelhoff added the BEP label Jul 1, 2020
@sappelhoff sappelhoff changed the title [WIP] BEP 011: Structural derivatives BEP 011: Structural derivatives May 22, 2021
@sappelhoff sappelhoff marked this pull request as draft May 22, 2021
@rwblair rwblair mentioned this pull request Apr 21, 2022
| flat | The flattened surface (used for visualization) |

`space` filename keyword is restricted to
[Surface Coordinate Spaces](../99-appendices/08-coordinate-systems.md#Surface)
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@rwblair rwblair Apr 21, 2022

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Currently there is no header for #Surface or #Volume to land on at ../99-appendices/08-coordinate-systems.md

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