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Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing #235

Merged
merged 70 commits into from
Mar 29, 2023
Merged

Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing #235

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d470dba
Use BolusCutOffDelayTime for PASL data.
tsalo Mar 15, 2023
bab13cd
Add fix to vanilla CBF calculation.
tsalo Mar 15, 2023
536e1fa
Use nilearn for masking and unmasking.
tsalo Mar 15, 2023
6ca94c9
Update misc.py
tsalo Mar 15, 2023
cca03a2
Update misc.py
tsalo Mar 15, 2023
2420dfe
Merge remote-tracking branch 'upstream/main' into pasl-bug
tsalo Mar 15, 2023
cd2a1b9
Move compute_cbf into ComputeCBF.
tsalo Mar 15, 2023
9578fcf
Update cbf_computation.py
tsalo Mar 15, 2023
da04ac8
Update cbf_computation.py
tsalo Mar 15, 2023
27d8137
Update cbf_computation.py
tsalo Mar 15, 2023
1c55346
Update cbf_computation.py
tsalo Mar 15, 2023
acd5b8b
Remove logger messages.
tsalo Mar 15, 2023
74e031a
Require BCOF be True for PASL across CBF methods.
tsalo Mar 16, 2023
911704f
Remove unused att output.
tsalo Mar 16, 2023
ac627ee
Remove unused BASIL inputs.
tsalo Mar 16, 2023
c4e1899
Remove more inputs that are really outputs.
tsalo Mar 16, 2023
a14b816
Update ge.py
tsalo Mar 16, 2023
b70f4bc
Check ASLT more explicitly.
tsalo Mar 16, 2023
bcc30a1
Expect a list if technique is Q2TIPS.
tsalo Mar 16, 2023
240255a
Remove duplicate references.
tsalo Mar 17, 2023
0fa6415
Work around nilearn-made singleton dims.
tsalo Mar 17, 2023
b6eb752
Pin nilearn version.
tsalo Mar 17, 2023
08f2164
Improve comment.
tsalo Mar 17, 2023
41476af
Clean up CBF calculation.
tsalo Mar 20, 2023
44a0cbe
Fix PASL CSF calculation.
tsalo Mar 20, 2023
74a998e
Improve comments.
tsalo Mar 20, 2023
dfb2d3c
Improve ComputeCBF input/output names.
tsalo Mar 20, 2023
06406d6
Improve documentation again.
tsalo Mar 20, 2023
d73b221
Remove unnecessary fields from BibTeX entries.
tsalo Mar 20, 2023
9979d4c
Document ComputeCBF.
tsalo Mar 20, 2023
a0adad9
Update cbf_computation.py
tsalo Mar 20, 2023
573e396
Improve variable naming.
tsalo Mar 24, 2023
e0fa265
Change a lot of variable names.
tsalo Mar 24, 2023
e81a4d0
Hopefully support QUIPSS and Q2TIPS.
tsalo Mar 27, 2023
8068dbf
Update.
tsalo Mar 27, 2023
de6a9a4
Add a message about Q2TIPS.
tsalo Mar 27, 2023
f4f74fd
Merge remote-tracking branch 'upstream/main' into pasl-bug
tsalo Mar 27, 2023
2fd718c
Add a test for ComputeCBF.
tsalo Mar 27, 2023
13530ad
Update test_interfaces_cbf_computation.py
tsalo Mar 27, 2023
dd5bcab
Update test_interfaces_cbf_computation.py
tsalo Mar 27, 2023
4c5bc12
Just use tmpdir.
tsalo Mar 27, 2023
8828ba5
Update test_interfaces_cbf_computation.py
tsalo Mar 27, 2023
a6ea23e
Add CASL labeling efficiency value.
tsalo Mar 27, 2023
183ccb5
Replace T1blood formula with hardcoded values.
tsalo Mar 27, 2023
567b926
Drop check within pcasl_or_pasl. Checked elsewhere.
tsalo Mar 27, 2023
0d6f4f2
Push T1blood change to another PR.
tsalo Mar 28, 2023
915fede
Modify PLDs in metadata during deltam selection.
tsalo Mar 28, 2023
741e435
Try fixing the PLDs.
tsalo Mar 28, 2023
ce385b2
Add logger messages.
tsalo Mar 28, 2023
24bc1ed
Update cbf_computation.py
tsalo Mar 28, 2023
cc976f1
Update cbf_computation.py
tsalo Mar 28, 2023
c27ded8
Update cbf_computation.py
tsalo Mar 28, 2023
229f3d5
Update cbf_computation.py
tsalo Mar 28, 2023
bdaf2a3
Fix?
tsalo Mar 28, 2023
a01e2a4
Add another integration test.
tsalo Mar 28, 2023
a97598c
Update test.
tsalo Mar 28, 2023
a279bc6
Skip new test for now.
tsalo Mar 28, 2023
d970d7d
Try to simplify the CBF workflows.
tsalo Mar 28, 2023
4b60eb1
Fix bugs hopefully.
tsalo Mar 28, 2023
a811b4a
Move connections around a bit.
tsalo Mar 28, 2023
e1cde1e
Fix bug maybe.
tsalo Mar 28, 2023
757346e
Expect failures on multi-PLD data.
tsalo Mar 28, 2023
150ea6a
Fix test.
tsalo Mar 28, 2023
c8b94ac
Fix things more.
tsalo Mar 28, 2023
a32304f
Update cbf_computation.py
tsalo Mar 28, 2023
de3017f
Fix...
tsalo Mar 28, 2023
d5634e6
Update cbf_computation.py
tsalo Mar 29, 2023
67f1483
Use first BolusCutOffDelayTime for Q2TIPS w BASIL.
tsalo Mar 29, 2023
b7113c0
Split things up a bit.
tsalo Mar 29, 2023
7b63aec
Disable Q2TIPS.
tsalo Mar 29, 2023
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