Implement general kinetic model for multi-PLD data

.circleci/config.yml

@@ -339,6 +339,8 @@ jobs:
           root: /src/coverage
           paths:
               - .coverage.examples_pasl_multipld
+    # The resource_class feature allows configuring CPU and RAM resources for each job. Different resource classes are available for different executors. https://circleci.com/docs/2.0/configuration-reference/#resourceclass
+    resource_class: large
 
   qtab:
     <<: *dockersetup

LICENSE.md

@@ -25,30 +25,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-## External code
-
-### aslprep.utils.misc.estimate_att_pcasl
-
-MIT License
-
-Copyright (c) 2023 willtack
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

aslprep/data/aslprep_bids_config.json

@@ -37,9 +37,9 @@
     "sub-{subject}[/ses-{session}]/[{datatype<func|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>|.tsv.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func|perf>|func}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors|timeseries>|timeseries}{extension<.json|.tsv|.csv|>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<confounds>}{extension<.tsv|.json>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.csv|.tsv>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|att|cbf>}{extension<.dtseries.nii|.dscalar.nii|.json|.dscalar.json|.dtseries.json|.func.gii|.func.json>|.dtseries.nii}",
-    "sub-{subject}[/ses-{session}]/{datatype<figures>|figures}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|basil|score|scrub|pvc|mask>}{extension<.svg|.png|.html>|.svg}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|abat|abv|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.csv|.tsv>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|abat|abv|att|cbf>}{extension<.dtseries.nii|.dscalar.nii|.json|.dscalar.json|.dtseries.json|.func.gii|.func.json>|.dtseries.nii}",
+    "sub-{subject}[/ses-{session}]/{datatype<figures>|figures}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|abat|abv|att|cbf|basil|score|scrub|pvc|mask>}{extension<.svg|.png|.html>|.svg}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5|.json>}",

aslprep/data/boilerplate.bib

@@ -557,27 +557,6 @@ @article{groves2009combined
   publisher={Elsevier}
 }
 
-@article{dai2012reduced,
-  title={Reduced resolution transit delay prescan for quantitative continuous arterial spin labeling perfusion imaging},
-  author={Dai, Weiying and Robson, Philip M and Shankaranarayanan, Ajit and Alsop, David C},
-  journal={Magnetic resonance in medicine},
-  volume={67},
-  number={5},
-  pages={1252--1265},
-  year={2012},
-  publisher={Wiley Online Library}
-}
-
-@article{wang2013multi,
-  title={Multi-delay multi-parametric arterial spin-labeled perfusion MRI in acute ischemic stroke—comparison with dynamic susceptibility contrast enhanced perfusion imaging},
-  author={Wang, Danny JJ and Alger, Jeffry R and Qiao, Joe X and Gunther, Matthias and Pope, Whitney B and Saver, Jeffrey L and Salamon, Noriko and Liebeskind, David S and UCLA Stroke Investigators and others},
-  journal={NeuroImage: Clinical},
-  volume={3},
-  pages={1--7},
-  year={2013},
-  publisher={Elsevier}
-}
-
 @article{clement2022asl,
   title={ASL-BIDS, the brain imaging data structure extension for arterial spin labeling},
   author={Clement, Patricia and Castellaro, Marco and Okell, Thomas W and Thomas, David L and Vandemaele, Pieter and Elgayar, Sara and Oliver-Taylor, Aaron and Kirk, Thomas and Woods, Joseph G and Vos, Sjoerd B and others},
@@ -615,31 +594,6 @@ @article{wang2005amplitude
   doi={10.1148/radiol.2351031663}
 }
 
-@article{fan2017long,
-  title={Long-delay arterial spin labeling provides more accurate cerebral blood flow measurements in moyamoya patients: a simultaneous positron emission tomography/MRI study},
-  author={Fan, Audrey P and Guo, Jia and Khalighi, Mohammad M and Gulaka, Praveen K and Shen, Bin and Park, Jun Hyung and Gandhi, Harsh and Holley, Dawn and Rutledge, Omar and Singh, Prachi and others},
-  journal={Stroke},
-  volume={48},
-  number={9},
-  pages={2441--2449},
-  year={2017},
-  publisher={Am Heart Assoc},
-  url={https://doi.org/10.1161/STROKEAHA.117.017773},
-  doi={10.1161/STROKEAHA.117.017773}
-}
-
-@article{juttukonda2021characterizing,
-  title={Characterizing cerebral hemodynamics across the adult lifespan with arterial spin labeling MRI data from the Human Connectome Project-Aging},
-  author={Juttukonda, Meher R and Li, Binyin and Almaktoum, Randa and Stephens, Kimberly A and Yochim, Kathryn M and Yacoub, Essa and Buckner, Randy L and Salat, David H},
-  journal={Neuroimage},
-  volume={230},
-  pages={117807},
-  year={2021},
-  publisher={Elsevier},
-  url={https://doi.org/10.1016/j.neuroimage.2021.117807},
-  doi={10.1016/j.neuroimage.2021.117807}
-}
-
 @article{noguchi2015technical,
   title={A technical perspective for understanding quantitative arterial spin-labeling MR imaging using Q2TIPS},
   author={Noguchi, Tomoyuki and Nishihara, Masashi and Hara, Yukiko and Hirai, Tetsuyoshi and Egashira, Yoshiaki and Azama, Shinya and Irie, Hiroyuki},
@@ -852,3 +806,13 @@ @article{topup
     doi = {10.1016/S1053-8119(03)00336-7},
     url = {https://www.sciencedirect.com/science/article/pii/S1053811903003367}
 }
+
+@article{woods2023recommendations,
+  title={Recommendations for quantitative cerebral perfusion MRI using multi-timepoint arterial spin labeling: Acquisition, quantification, and clinical applications},
+  author={Woods, Joseph G and Achten, Eric and Asllani, Iris and Bolar, Divya S and Dai, Weiying and Detre, John A and Fan, Audrey P and Fern{\'a}ndez-Seara, Maria and Golay, Xavier and G{\"u}nther, Matthias and Guo, Jia and Hernandez-Garcia, Luis and Ho, Mai-Lan and Juttukonda, Meher R. and Lu, Hanzhang and MacIntosh, Bradley J. and Madhuranthakam, Ananth J. and Mutsaerts, Henk J.M.M. and Okell, Thomas W. and Parkes, Laura M. and Pinter, Nandor and Pinto, Joana and Qin, Qin and Smits, Marion and Suzuki, Yuriko and Thomas, David L. and van Osch, Matthias J.P. and Wang, Danny J.J. and Warnert, Esther A.H. and Zaharchuk, Greg and Zelaya, Fernando and Zhao, Moss and Chappell, Michael A.},
+  year={2023},
+  journal={OSF Preprints},
+  publisher={OSF Preprints},
+  doi={10.31219/osf.io/4tskr},
+  url={https://doi.org/10.31219/osf.io/4tskr},
+}