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

* Start drafting code to estimate ATT.

* Keep working on multi-PLD.

* Document methods a bit.

* More work.

* Keep working on ATT calculation.

* Allow multi-PLD data.

* Let the tests run.

* Update cbf_computation.py

* Update cbf_computation.py

* Update cbf_computation.py

* Update gitignore.

* Clean up config file a bit.

* Output ATT and rename att to att_basil.

* Only output CBF time series for single-PLD data

* Expect test_examples_pasl_multipld to fail.

* Continue with conditionals.

* Fix connections and tests.

* Update expected outputs.

Also disable scorescrub for multi-PLD data.

* Update cbf.py

* Update test_interfaces_cbf_computation.py

* Try adjusting the lists of expected connections.

* Update registration.py

* Fix errors.

* Update cbf_computation.py

* Expect correct error message.

* Update misc.py

* Update tests.

* Fix bug?

* Update test_cli.py

* Just stop on first crash.

* Update misc.py

* Try fixing the CBF calculation.

* Update misc.py

* Update misc.py

* Update misc.py

* Hopefully fix bug.

* Update cbf_computation.py

* Require output files for BASIL.

* Use nodes to extract info.

* Update misc.py

* Update expected_outputs_examples_pcasl_multipld.txt

* Improve documentation.

* Update workflows.rst

* Update workflows.rst

* Update workflows.rst

* Update workflows.rst

* Update boilerplate.bib

* Support single-PLD Q2TIPS.

* Fix typo.

* Update workflows.rst

* Update license info.

* Update workflows.rst

* Update misc.py

* Update misc.py

* Keep improving.

* Add license info for sdcflows and niworkflows.

* Update cbf.py

* Update workflows.rst

* Update .gitignore

* Refactor T1-estimation function.

* Update documentation.

* Update workflows.rst

* Update workflows.rst

* Update workflows.rst

* Update workflows.rst

* Restrict CBF plot values to -20 to 100.

* Update plotting.py

* Update plotting.py

* Update plotting.py

* X-PLD to X-delay.

* Update workflow description.

* Fix.

* Update cbf.py

* Update cbf_computation.py

* Update test_cli.py

* Update test_cli.py

* Update things.

* Update qc.py

* Update test_cli.py

* Update cbf.py

* Update cbf_computation.py

* Start working on shifted PLDs.

* Update test_interfaces_cbf_computation.py

* Update test_interfaces_cbf_computation.py

* Update test_interfaces_cbf_computation.py

* Add smoke tests for ATT estimation.

* Update test_utils_misc.py

* Update misc.py

* Move local test file.

* Update run_local_tests.py

* Just loop over voxels.

It's the least clever solution, but at least it should work.

* Fix tests.

* Fix other tests.

* Remove logger warnings.

* Update test 002 data.

* Update other test datasets.

* Update test_002 dataset.

* Adapt Split.

* Fix.

* Update misc.py

* Update cbf.py

* Update cbf.py

* Split up utils.misc.

* Rename cbf_computation to cbf.

* Work on improving CBF calculation documentation.

* Update workflows.rst

* Update docstrings.

* Revert mistake.

.circleci/config.yml

@@ -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
 
@@ -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
 
@@ -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
 
@@ -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
 
@@ -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
 
@@ -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
 
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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