-
Notifications
You must be signed in to change notification settings - Fork 157
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
BEP 011: Structural derivatives #518
base: master
Are you sure you want to change the base?
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.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
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.
Choose a reason for hiding this comment
The 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 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.
Choose a reason for hiding this comment
The 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.
| `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 comment
The reason will be displayed to describe this comment to others. Learn more.
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.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
+1 on this, since map
should be for quantitative outputs.
| 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.
Choose a reason for hiding this comment
The 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
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