Quick question about the space
entity for BIDS derivatives, and for masks in particular (partial duplicate of this topic, just asking for more specific clarification).
- The section about masks says
space
should be orig
if there hasn’t been a transformation.
- The definition of the
space
entitity says space
come from one of the modality specific lists in this appendix. The appendix says that images not registered to a standard template coordinate space can use one of the following for space
: individual
, study
, or scanner
(implicit default, and space
should just be omitted in this case). Notably, orig
is not included.
Is the use of orig
actually forbidden by the spec like the second point above seems to imply, or am I missing something (or is this just a case of derivatives not being strictly specified)? Thanks for your help!
I read that as an internal consistency in the spec. @effigies do you agree?
Also this makes me realize the space entity definition is too MEEG specific and needs to be broaden.
Yeah, it seems like an inconsistency. Sorry, I don’t have time to edit this into a really coherent post, so here are some thoughts:
-
IIRC space-orig
has generally been treated as an implicit space, so it’s just a way of saying that the image is not registered to any other image, which is the default assumption when working with data. I guess this is equivalent to “scanner”. This gets nasty in the context of masks, because they’re generally derived from an anatomical image, and that anatomical image may be in scanner space, you may decide that that anatomical image defines “subject space” (without changing it from its scanner space).
-
All in all, spaces are messy. It’s easy enough to make a convention for your pipeline, but very difficult to make a convention that will be unambiguous across pipelines.
-
Using space-orig
seems fine, semantically, but I would be careful about over-tagging. It doesn’t seem to add anything, so could safely be omitted. See Filenames richness versus distinctness.
-
In any case, the space entity label is permitted to be any string, as long as you provide a SpatialReference
metadata field. Only the listed templates are supposed to be exempt. It would probably make sense to exempt orig
from that as well.
Thanks for the responses! The context here was writing a BIDS app that takes (in part) a mask and associated image as input, and trying to figure out what values for space
I should accept. I guess broadly the answer in my case is to permit any (or no) space
label as long as it isn’t one of the standard template spaces.
Just as a wishlist/suggestion for resolving the inconsistencies in the spec:
- “the space entity label is permitted to be any string” seems to contradict “The
<label>
MUST be taken from one of the modality specific lists in the Coordinate Systems Appendix” from the entities appendix.
- Clarifying the recommendations between use of
orig
and scanner
in the coordinate systems appendix and masks section would be helpful.
Thanks again for your help!
Will try to open an issue on the bids specification repo to clarify some of the points mentioned here. But I am traveling at the moment.
So @tristankk feel free to open one and reference this thread.
For reference, I’ve gone ahead and opened an issue on this topic on the BIDS specification repo.