-
Notifications
You must be signed in to change notification settings - Fork 59
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
MT/ihMT scripts: cleanup and adding B1+ correction #870
Conversation
Hello @karanphil, Thank you for updating !
Comment last updated at 2024-02-21 16:05:10 UTC |
Build passed ! Good Job 🍻 ! |
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #870 +/- ##
===========================================
+ Coverage 1.95% 68.17% +66.22%
===========================================
Files 384 387 +3
Lines 13876 20865 +6989
Branches 1754 3213 +1459
===========================================
+ Hits 271 14225 +13954
+ Misses 13561 5358 -8203
- Partials 44 1282 +1238
|
Build passed ! Good Job 🍻 ! |
Build passed ! Good Job 🍻 ! |
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.
Some details for Warning messages, otherwise it's good for me!
INFO:root:Scilpy version: 1.7.dev0
WARNING:root:Repetition time found in mton.json does not seem to be given in seconds. MTsat results might be affected.
INFO:root:Loaded mton_Warped.nii.gz of shape (180, 240, 240) and data_type float64.
INFO:root:Loaded mtoff_Warped.nii.gz of shape (180, 240, 240) and data_type float64.
INFO:root:Loaded mt_t1.nii.gz of shape (180, 240, 240) and data_type int16.
Build passed ! Good Job 🍻 ! |
Build passed ! Good Job 🍻 ! |
Quick description
Hi,
I added B1+ field inhomogeneity correction to
scil_mti_maps_MT.py
andscil_mti_maps_ihMT.py
. Doing so, I also cleaned up those scripts and the functions they call inscilpy.reconst.mti
. I also added a script (scil_mti_adjust_B1_header.py
) to correct the bug in the B1 map header, with the scaling issue. There is now a new correction method for B1+, called "model_based" and it requires .mat files obtained with Matlab at the moment. I will send these to the reviewers.I tested the scripts and they produce the same results as before (without B1 correction). @Manonedde, you should still test them to make sure everything works fine.
Feel free to comment on the choices I made ;)
This PR doesn't have to be merged quickly.
...
Type of change
Check the relevant options.
Provide data, screenshots, command line to test (if relevant)
...
Checklist