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Support single-PLD Q2TIPS PASL and multi-PLD PCASL #268

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May 25, 2023
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760226f
Start drafting code to estimate ATT.
tsalo Apr 19, 2023
f0c4b39
Keep working on multi-PLD.
tsalo Apr 19, 2023
41cf8f0
Document methods a bit.
tsalo Apr 19, 2023
e54fbb4
More work.
tsalo Apr 19, 2023
9e23d41
Keep working on ATT calculation.
tsalo Apr 20, 2023
369223c
Allow multi-PLD data.
tsalo Apr 20, 2023
44a3b0b
Let the tests run.
tsalo Apr 20, 2023
6190a19
Update cbf_computation.py
tsalo Apr 20, 2023
cbcabe0
Update cbf_computation.py
tsalo Apr 20, 2023
3a81ac7
Update cbf_computation.py
tsalo Apr 21, 2023
90ce1cb
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo Apr 21, 2023
55f5942
Update gitignore.
tsalo Apr 21, 2023
84c05d2
Clean up config file a bit.
tsalo Apr 21, 2023
32617d7
Output ATT and rename att to att_basil.
tsalo Apr 21, 2023
30147dd
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo Apr 21, 2023
51707ad
Only output CBF time series for single-PLD data
tsalo Apr 21, 2023
fe013ea
Expect test_examples_pasl_multipld to fail.
tsalo Apr 21, 2023
2b2ba39
Continue with conditionals.
tsalo Apr 21, 2023
19cc430
Fix connections and tests.
tsalo Apr 21, 2023
392c9ba
Update expected outputs.
tsalo Apr 21, 2023
655e380
Update cbf.py
tsalo Apr 21, 2023
9f7a9fe
Update test_interfaces_cbf_computation.py
tsalo Apr 21, 2023
c040ed4
Try adjusting the lists of expected connections.
tsalo Apr 21, 2023
78f3e24
Update registration.py
tsalo Apr 21, 2023
2089d0d
Fix errors.
tsalo Apr 21, 2023
90129b1
Update cbf_computation.py
tsalo Apr 21, 2023
b05bd51
Expect correct error message.
tsalo Apr 21, 2023
666f43d
Update misc.py
tsalo Apr 21, 2023
1a9930a
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo Apr 21, 2023
c22c7a7
Update tests.
tsalo Apr 21, 2023
c5cf657
Fix bug?
tsalo Apr 24, 2023
62930cc
Update test_cli.py
tsalo Apr 24, 2023
12ad322
Just stop on first crash.
tsalo Apr 24, 2023
ba946ac
Update misc.py
tsalo Apr 24, 2023
c613b19
Try fixing the CBF calculation.
tsalo Apr 24, 2023
82cde45
Update misc.py
tsalo Apr 24, 2023
26f02d5
Update misc.py
tsalo Apr 24, 2023
e092239
Update misc.py
tsalo Apr 24, 2023
6bb1c39
Hopefully fix bug.
tsalo Apr 24, 2023
ffe773e
Update cbf_computation.py
tsalo Apr 24, 2023
e0f5d17
Require output files for BASIL.
tsalo Apr 24, 2023
925a6a9
Use nodes to extract info.
tsalo Apr 24, 2023
3c88f02
Update misc.py
tsalo Apr 24, 2023
334d3c8
Update expected_outputs_examples_pcasl_multipld.txt
tsalo Apr 25, 2023
4bdd979
Improve documentation.
tsalo Apr 25, 2023
5d4e416
Update workflows.rst
tsalo Apr 25, 2023
d744b4d
Update workflows.rst
tsalo Apr 25, 2023
e0334a2
Update workflows.rst
tsalo Apr 25, 2023
d3c6b74
Update workflows.rst
tsalo Apr 25, 2023
f628f25
Update boilerplate.bib
tsalo Apr 25, 2023
ebc9776
Support single-PLD Q2TIPS.
tsalo Apr 25, 2023
297b46c
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo Apr 25, 2023
8a6ee0e
Fix typo.
tsalo Apr 25, 2023
df8e3dc
Update workflows.rst
tsalo Apr 26, 2023
ea5876e
Update license info.
tsalo Apr 27, 2023
292dedf
Update workflows.rst
tsalo Apr 27, 2023
51fcd07
Update misc.py
tsalo Apr 27, 2023
4c4fe46
Update misc.py
tsalo Apr 27, 2023
fad2d95
Keep improving.
tsalo Apr 27, 2023
7e4f0fd
Add license info for sdcflows and niworkflows.
tsalo Apr 27, 2023
cd24c2c
Update cbf.py
tsalo Apr 27, 2023
9ffb86a
Update workflows.rst
tsalo Apr 27, 2023
9f90eb7
Update .gitignore
tsalo May 2, 2023
4ab23ca
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 9, 2023
87f91f9
Refactor T1-estimation function.
tsalo May 10, 2023
b02b14e
Update documentation.
tsalo May 11, 2023
0465715
Update workflows.rst
tsalo May 11, 2023
a0f33d7
Update workflows.rst
tsalo May 11, 2023
fa078e1
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 11, 2023
ccba0b4
Update workflows.rst
tsalo May 11, 2023
68162cf
Update workflows.rst
tsalo May 11, 2023
e6dd200
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 12, 2023
7bb1685
Restrict CBF plot values to -20 to 100.
tsalo May 12, 2023
83133cc
Update plotting.py
tsalo May 12, 2023
f95432d
Update plotting.py
tsalo May 12, 2023
b9708e5
Update plotting.py
tsalo May 12, 2023
dace488
X-PLD to X-delay.
tsalo May 12, 2023
f191687
Update workflow description.
tsalo May 12, 2023
fd520f6
Fix.
tsalo May 12, 2023
51e8c29
Update cbf.py
tsalo May 12, 2023
5aa52d2
Update cbf_computation.py
tsalo May 12, 2023
9a1c798
Update test_cli.py
tsalo May 12, 2023
9303852
Update test_cli.py
tsalo May 12, 2023
c056fa8
Update things.
tsalo May 12, 2023
6b804b7
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 16, 2023
b36a977
Update qc.py
tsalo May 16, 2023
b02a0dd
Update test_cli.py
tsalo May 16, 2023
dbaa4a5
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 16, 2023
8ec9ea1
Update cbf.py
tsalo May 16, 2023
17aea7d
Update cbf_computation.py
tsalo May 17, 2023
ad2c58a
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 17, 2023
8c447f1
Start working on shifted PLDs.
tsalo May 17, 2023
42cb2f3
Update test_interfaces_cbf_computation.py
tsalo May 18, 2023
0133888
Update test_interfaces_cbf_computation.py
tsalo May 18, 2023
fbaf13a
Update test_interfaces_cbf_computation.py
tsalo May 18, 2023
ee51a2a
Add smoke tests for ATT estimation.
tsalo May 18, 2023
93cb181
Update test_utils_misc.py
tsalo May 18, 2023
241c530
Update misc.py
tsalo May 22, 2023
0a082fc
Move local test file.
tsalo May 22, 2023
4f0ace7
Update run_local_tests.py
tsalo May 22, 2023
536bcd3
Just loop over voxels.
tsalo May 22, 2023
ed25c01
Fix tests.
tsalo May 22, 2023
9d4d1d1
Fix other tests.
tsalo May 22, 2023
dc01dd5
Remove logger warnings.
tsalo May 22, 2023
992d592
Update test 002 data.
tsalo May 22, 2023
bcc5420
Update other test datasets.
tsalo May 22, 2023
3344123
Update test_002 dataset.
tsalo May 22, 2023
9c2897e
Adapt Split.
tsalo May 22, 2023
d9c15e1
Fix.
tsalo May 22, 2023
3a28bfb
Update misc.py
tsalo May 23, 2023
71717e4
Merge remote-tracking branch 'upstream/main' into multi-pld
tsalo May 23, 2023
143709b
Update cbf.py
tsalo May 23, 2023
9f81b6d
Update cbf.py
tsalo May 23, 2023
f1b6079
Split up utils.misc.
tsalo May 23, 2023
1d801f0
Rename cbf_computation to cbf.
tsalo May 24, 2023
f73c2a7
Work on improving CBF calculation documentation.
tsalo May 24, 2023
070d2ac
Update workflows.rst
tsalo May 25, 2023
828b3ad
Update docstrings.
tsalo May 25, 2023
5812d8a
Revert mistake.
tsalo May 25, 2023
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44 changes: 22 additions & 22 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -38,15 +38,15 @@ jobs:
steps:
- checkout
- restore_cache:
key: examples_pcasl_singlepld-v1
key: examples_pcasl_singlepld-v2
- run: *runinstall
- run:
name: Get test data and smriprep from box
command: |
cd /src/aslprep/.circleci
python get_data.py ${PWD}/data examples_pcasl_singlepld
- save_cache:
key: examples_pcasl_singlepld-v1
key: examples_pcasl_singlepld-v2
paths:
- /src/aslprep/.circleci/data

Expand All @@ -55,15 +55,15 @@ jobs:
steps:
- checkout
- restore_cache:
key: examples_pcasl_multipld-v1
key: examples_pcasl_multipld-v2
- run: *runinstall
- run:
name: Get test data and smriprep from box
command: |
cd /src/aslprep/.circleci
python get_data.py ${PWD}/data examples_pcasl_multipld
- save_cache:
key: examples_pcasl_multipld-v1
key: examples_pcasl_multipld-v2
paths:
- /src/aslprep/.circleci/data

Expand All @@ -72,15 +72,15 @@ jobs:
steps:
- checkout
- restore_cache:
key: examples_pasl_multipld-v1
key: examples_pasl_multipld-v2
- run: *runinstall
- run:
name: Get test data and smriprep from box
command: |
cd /src/aslprep/.circleci
python get_data.py ${PWD}/data examples_pasl_multipld
- save_cache:
key: examples_pasl_multipld-v1
key: examples_pasl_multipld-v2
paths:
- /src/aslprep/.circleci/data

Expand All @@ -89,15 +89,15 @@ jobs:
steps:
- checkout
- restore_cache:
key: test_001-v1
key: test_001-v2
- run: *runinstall
- run:
name: Get test data and smriprep from box
command: |
cd /src/aslprep/.circleci
python get_data.py ${PWD}/data test_001
- save_cache:
key: test_001-v1
key: test_001-v2
paths:
- /src/aslprep/.circleci/data

Expand All @@ -106,15 +106,15 @@ jobs:
steps:
- checkout
- restore_cache:
key: test_002-v1
key: test_002-v3
- run: *runinstall
- run:
name: Get test data and smriprep from box
command: |
cd /src/aslprep/.circleci
python get_data.py ${PWD}/data test_002
- save_cache:
key: test_002-v1
key: test_002-v3
paths:
- /src/aslprep/.circleci/data

Expand All @@ -123,15 +123,15 @@ jobs:
steps:
- checkout
- restore_cache:
key: test_003-v1
key: test_003-v2
- run: *runinstall
- run:
name: Get test data and smriprep from box
command: |
cd /src/aslprep/.circleci
python get_data.py ${PWD}/data test_003
- save_cache:
key: test_003-v1
key: test_003-v2
paths:
- /src/aslprep/.circleci/data

Expand All @@ -148,7 +148,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: examples_pcasl_singlepld-v1
key: examples_pcasl_singlepld-v2
- run: *runinstall
- run:
name: Run full aslprep on examples_pcasl_singlepld_philips dataset
Expand Down Expand Up @@ -179,7 +179,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: examples_pcasl_singlepld-v1
key: examples_pcasl_singlepld-v2
- run: *runinstall
- run:
name: Run full aslprep on examples_pcasl_singlepld_siemens dataset
Expand Down Expand Up @@ -210,7 +210,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: examples_pcasl_singlepld-v1
key: examples_pcasl_singlepld-v2
- run: *runinstall
- run:
name: Run full aslprep on examples_pcasl_singlepld dataset
Expand Down Expand Up @@ -241,7 +241,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: examples_pcasl_multipld-v1
key: examples_pcasl_multipld-v2
- run: *runinstall
- run:
name: Run full aslprep on examples_pcasl_multipld dataset
Expand Down Expand Up @@ -272,7 +272,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: examples_pasl_multipld-v1
key: examples_pasl_multipld-v2
- run: *runinstall
- run:
name: Run full aslprep on examples_pasl_multipld dataset
Expand Down Expand Up @@ -303,7 +303,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: test_001-v1
key: test_001-v2
- run: *runinstall
- run:
name: Run full aslprep on test_001 dataset
Expand Down Expand Up @@ -334,7 +334,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: test_002-v1
key: test_002-v3
- run: *runinstall
- run:
name: Run full aslprep on test_002 dataset
Expand Down Expand Up @@ -365,7 +365,7 @@ jobs:
circleci step halt
fi
- restore_cache:
key: test_003-v1
key: test_003-v2
- run: *runinstall
- run:
name: Run full aslprep on test_003 dataset
Expand Down Expand Up @@ -396,9 +396,9 @@ jobs:
circleci step halt
fi
- restore_cache:
key: test_001-v1
key: test_001-v2
- restore_cache:
key: test_003-v1
key: test_003-v2
- run: *runinstall
- run:
name: Run pytest on the tests directory
Expand Down
27 changes: 0 additions & 27 deletions LICENSE

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