Skip to content
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.

Sign up for GitHub

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

Jump to bottom

function to calculate overlap with labelfield #16

Open
jefferis opened this issue Jun 19, 2014 · 5 comments
Open

function to calculate overlap with labelfield #16

jefferis opened this issue Jun 19, 2014 · 5 comments
Labels
enhancement question

Comments

@jefferis
Copy link
Contributor

Would like either a function or simple examples showing how to calculate overlap with a label field.

Should we be including the VFB label field in e.g. JFRC2, FCWB, T1 and IS2 space?
@jefferis
Copy link
Contributor Author

Incidentally we could translate overlap from the space of the data collection to JFRC2 space by the use of Jacobian determinants for the bridging registration.

@jefferis
Copy link
Contributor Author

Probably belongs in nat.templatebrains or even in nat at this point

@jefferis
Copy link
Contributor Author

jefferis commented Aug 2, 2014

At its simplest, this would take a thresholded image and a label field and return a data.frame with counts of each label and its overlap.

@jefferis
Copy link
Contributor Author

jefferis commented Aug 3, 2014

OK I think this should be implemented as nat::cmtk.statistics (translating nat.as::CMTKStatistics) + a function in nat.templatebrains that coordinates thesholding etc.

jefferis added a commit to natverse/nat that referenced this issue Aug 4, 2014
@jefferis
Merge branch 'feature/cmtk.statistics'
8d2d7c6 
* feature/cmtk.statistics:
  Teach cmtk.statistics to pass ... to cmtk tool
  fix typo in help
  remove exe argument and roxygenise
  rename to cmtk.statistics
  Verbatim copy of CMTKStatistics from nat.as
* part way to closing natverse/nat.flybrains#16
@jefferis
Copy link
Contributor Author

So the status of this is that nat now has a nat::cmtk.statistics function as of natverse/nat@8d2d7c6 but the other part of the solution (coordinating the thresholding) is not yet defined or implemented.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement question
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@jefferis