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Merge remote-tracking branch 'upstream/master' into enh/fs_long
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bpinsard committed Jan 15, 2024
2 parents 0ebd309 + de72651 commit 217a350
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8 changes: 0 additions & 8 deletions .circleci/ds005_fasttrack_outputs.txt
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Expand Up @@ -23,16 +23,12 @@ sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
sub-01/func
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
Expand All @@ -45,16 +41,12 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
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8 changes: 0 additions & 8 deletions .circleci/ds005_outputs.txt
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Expand Up @@ -43,16 +43,12 @@ sub-01/anat/sub-01_label-CSF_probseg.nii.gz
sub-01/anat/sub-01_label-GM_probseg.nii.gz
sub-01/anat/sub-01_label-WM_probseg.nii.gz
sub-01/func
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
Expand All @@ -65,16 +61,12 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
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4 changes: 0 additions & 4 deletions .circleci/ds005_partial_fasttrack_outputs.txt
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Expand Up @@ -51,16 +51,12 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
sub-01/func
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json
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4 changes: 0 additions & 4 deletions .circleci/ds005_partial_outputs.txt
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Expand Up @@ -73,16 +73,12 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
sub-01/func
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
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4 changes: 0 additions & 4 deletions .circleci/ds210_fasttrack_outputs.txt
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Expand Up @@ -31,8 +31,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.json
sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.json
sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
Expand All @@ -45,8 +43,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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4 changes: 0 additions & 4 deletions .circleci/ds210_outputs.txt
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Expand Up @@ -41,8 +41,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.json
sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.json
sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
Expand All @@ -55,8 +53,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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2 changes: 1 addition & 1 deletion .github/workflows/contrib.yml
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Expand Up @@ -32,7 +32,7 @@ jobs:
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
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4 changes: 2 additions & 2 deletions .github/workflows/pre-release.yml
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Expand Up @@ -27,7 +27,7 @@ jobs:
strategy:
matrix:
os: ['ubuntu-latest']
python-version: ['3.10', '3.11']
python-version: ['3.10', '3.11', '3.12']
install: ['pip']
check: ['tests']
pip-flags: ['PRE_PIP_FLAGS']
Expand All @@ -45,7 +45,7 @@ jobs:
- name: Install dependencies
run: .maint/ci/install_dependencies.sh
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
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4 changes: 2 additions & 2 deletions .github/workflows/stable.yml
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ jobs:
strategy:
matrix:
os: ['ubuntu-latest']
python-version: ['3.10', '3.11']
python-version: ['3.10', '3.11', '3.12']
install: ['pip']
check: ['tests']
pip-flags: ['']
Expand All @@ -48,7 +48,7 @@ jobs:
- name: Install dependencies
run: .maint/ci/install_dependencies.sh
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
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1 change: 1 addition & 0 deletions .maint/CONTRIBUTORS.md
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Expand Up @@ -32,6 +32,7 @@ Before every release, unlisted contributors will be invited again to add their n
| Liem | Franz | | 0000-0003-0646-4810 | URPP Dynamics of Healthy Aging, University of Zurich |
| Lurie | Daniel J. | | 0000-0001-8012-6399 | Department of Psychology, University of California, Berkeley |
| Ma | Feilong | | 0000-0002-6838-3971 | Dartmouth College: Hanover, NH, United States |
| Madison | Thomas | | 0000-0003-3030-6580 | Department of Pediatrics, University of Minnesota, MN, USA |
| Mentch | Jeff | | 0000-0002-7762-8678 | Speech & Hearing Bioscience & Technology Program, Harvard University |
| Moodie | Craig A. | | 0000-0003-0867-1469 | Department of Psychology, Stanford University |
| Naveau | Mikaël | | 0000-0001-6948-9068 | Cyceron, UMS 3408 (CNRS - UCBN), France |
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89 changes: 51 additions & 38 deletions .zenodo.json
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Expand Up @@ -8,12 +8,24 @@
"orcid": "0000-0002-1668-9629",
"type": "Researcher"
},
{
"affiliation": "Department of Pediatrics, University of Minnesota, MN, USA",
"name": "Madison, Thomas",
"orcid": "0000-0003-3030-6580",
"type": "Researcher"
},
{
"affiliation": "Florey Institute of Neuroscience and Mental Health",
"name": "Smith, Robert E.",
"orcid": "0000-0003-3636-4642",
"type": "Researcher"
},
{
"affiliation": "Neurospin, CEA",
"name": "Papadopoulos, Dimitri",
"orcid": "0000-0002-1242-8990",
"type": "Researcher"
},
{
"affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń",
"name": "Finc, Karolina",
Expand All @@ -26,18 +38,6 @@
"orcid": "0000-0002-6533-2909",
"type": "Researcher"
},
{
"affiliation": "Neurospin, CEA",
"name": "Papadopoulos, Dimitri",
"orcid": "0000-0002-1242-8990",
"type": "Researcher"
},
{
"affiliation": "Dartmouth College: Hanover, NH, United States",
"name": "Halchenko, Yaroslav O.",
"orcid": "0000-0003-3456-2493",
"type": "Researcher"
},
{
"affiliation": "Department of Neuroscience, University of Pennsylvania, PA, USA",
"name": "Tooley, Ursula A.",
Expand All @@ -51,9 +51,9 @@
"type": "Researcher"
},
{
"affiliation": "University of Texas at Austin",
"name": "de la Vega, Alejandro",
"orcid": "0000-0001-9062-3778",
"affiliation": "Dartmouth College: Hanover, NH, United States",
"name": "Halchenko, Yaroslav O.",
"orcid": "0000-0003-3456-2493",
"type": "Researcher"
},
{
Expand All @@ -63,9 +63,9 @@
"type": "Researcher"
},
{
"affiliation": "Montreal Neurological Institute, McGill University",
"name": "Urchs, Sebastian",
"orcid": "0000-0001-5504-8579",
"affiliation": "University of Texas at Austin",
"name": "de la Vega, Alejandro",
"orcid": "0000-0001-9062-3778",
"type": "Researcher"
},
{
Expand All @@ -75,9 +75,15 @@
"type": "Researcher"
},
{
"affiliation": "Charite Universitatsmedizin Berlin, Germany",
"name": "Waller, Lea",
"orcid": "0000-0002-3239-6957",
"affiliation": "Montreal Neurological Institute, McGill University",
"name": "Urchs, Sebastian",
"orcid": "0000-0001-5504-8579",
"type": "Researcher"
},
{
"affiliation": "Machine Learning Team, National Institute of Mental Health, USA",
"name": "Nielson, Dylan M.",
"orcid": "0000-0003-4613-6643",
"type": "Researcher"
},
{
Expand All @@ -86,6 +92,12 @@
"orcid": "0000-0002-2050-0614",
"type": "Researcher"
},
{
"affiliation": "Charite Universitatsmedizin Berlin, Germany",
"name": "Waller, Lea",
"orcid": "0000-0002-3239-6957",
"type": "Researcher"
},
{
"affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
"name": "Mentch, Jeff",
Expand All @@ -98,12 +110,6 @@
"orcid": "0000-0001-8012-6399",
"type": "Researcher"
},
{
"affiliation": "Department of Psychology, Columbia University",
"name": "Jacoby, Nir",
"orcid": "0000-0001-7936-9991",
"type": "Researcher"
},
{
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
"name": "Erramuzpe, Asier",
Expand Down Expand Up @@ -194,6 +200,18 @@
"orcid": "0000-0002-1652-9297",
"type": "Researcher"
},
{
"affiliation": "Department of Psychology, Columbia University",
"name": "Jacoby, Nir",
"orcid": "0000-0001-7936-9991",
"type": "Researcher"
},
{
"affiliation": "Department of Psychology, University of Washington",
"name": "Kruper, John",
"orcid": "0000-0003-0081-391X",
"type": "Researcher"
},
{
"affiliation": "URPP Dynamics of Healthy Aging, University of Zurich",
"name": "Liem, Franz",
Expand Down Expand Up @@ -301,19 +319,19 @@
"orcid": "0000-0002-1668-9629"
},
{
"affiliation": "Montreal Neurological Institute, McGill University",
"name": "DuPre, Elizabeth",
"orcid": "0000-0003-1358-196X"
"affiliation": "Department of Psychology, Florida International University",
"name": "Salo, Taylor",
"orcid": "0000-0001-9813-3167"
},
{
"affiliation": "Neuroscience Program, University of Iowa",
"name": "Kent, James D.",
"orcid": "0000-0002-4892-2659"
},
{
"affiliation": "Department of Psychology, Florida International University",
"name": "Salo, Taylor",
"orcid": "0000-0001-9813-3167"
"affiliation": "Montreal Neurological Institute, McGill University",
"name": "DuPre, Elizabeth",
"orcid": "0000-0003-1358-196X"
},
{
"affiliation": "Department of Psychology, Stanford University",
Expand All @@ -330,11 +348,6 @@
"name": "Blair, Ross W.",
"orcid": "0000-0003-3007-1056"
},
{
"affiliation": "Machine Learning Team, National Institute of Mental Health",
"name": "Nielson, Dylan M.",
"orcid": "0000-0003-4613-6643"
},
{
"affiliation": "Department of Psychology, Stanford University",
"name": "Poldrack, Russell A.",
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