-
Notifications
You must be signed in to change notification settings - Fork 4
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
Mdr t1 molli #228
base: dev
Are you sure you want to change the base?
Mdr t1 molli #228
Conversation
Note this is not a proper test - this file probably belongs elsewhere - maybe can become the basis for a tutorial on motion correction.
Hello @plaresmedima, thank you for updating!
Comment last updated at 2024-10-02 12:30:44 UTC |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #228 +/- ##
==========================================
- Coverage 97.97% 97.41% -0.57%
==========================================
Files 48 49 +1
Lines 4445 4484 +39
==========================================
+ Hits 4355 4368 +13
- Misses 90 116 +26 ☔ View full report in Codecov by Sentry. |
New mdr keyword in T1 class
Purpose: introduce a backwards compatible option to perform motion correction.
Usage: setting
mdr=True
inT1()
performs motion correction prior to computing the parameter maps. The default is False.Example: output with and without
mdr=True
(see below - note the sharper kidney outline whenmdr=True
). This example is generated by a new module test_mdreg.py, current in /tests. This may not be the appropriate place for it as it is not a proper unit test - more of an illustration.New attribute: This PR also introduces a new attribute
deformation_field
, which has the valueNone
whenmdr=False
New requirement: This brings in
mdreg
as a requirement, which ships with elastix and skimage.Note: There is currently still some inline comments that can be removed or shortened once they are addressed. For instance the current version still includes a hack to avoid the problem of autoselecting the wrong model, which still happened in this eample. This needs another solution but cannot be addressed at the level of mdr. There are also questions that are more an issue of design and the general approach in ukat, e.g. whether we expose coregistration options in the API or not.
See also Model Driven Registration #164 and MDR #183. The solution here should apply to other classes as well so we should be able to add mdr as an option everywhere with the same API (mdr=True keyword).