BEP 011: Structural derivatives #518
Conversation
| ## Reconstructed cortical surfaces | ||
|
|
||
| Reconstructed cortical surfaces should be stored as GIFTI files, and each | ||
| hemisphere should be stored separately. |
There was a problem hiding this comment.
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.
| ## 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 |
There was a problem hiding this comment.
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.
| <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) | |
There was a problem hiding this comment.
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 | |
There was a problem hiding this comment.
I think we've discussed changing this to:
| | `myelinmap` | Myelin map calculated from T1w to T2w ratio | | |
| | `T1wT2wratio`| T1w to T2w ratio, a proxy for myelination | |
There was a problem hiding this comment.
+1 on this, since map should be for quantitative outputs.
sappelhoff
changed the title
| | flat | The flattened surface (used for visualization) | | ||
|
|
||
| `space` filename keyword is restricted to | ||
| [Surface Coordinate Spaces](../99-appendices/08-coordinate-systems.md#Surface) |
There was a problem hiding this comment.
Currently there is no header for #Surface or #Volume to land on at ../99-appendices/08-coordinate-systems.md
|
maintenance note: added a link to the rendered BEP in the top message of this PR. |
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.
Link to the HTML rendered BEP: https://bids-specification--518.org.readthedocs.build/en/518/05-derivatives/04-structural-derivatives.html
cc @edickie @vsiless