Merge remote-tracking branch 'upstream/master' into enh/sep_anat_func…

…_report
nipreps · Jan 18, 2024 · 2d35de6 · 2d35de6
2 parents fc52e20 + 9568ccb
commit 2d35de6
Show file tree

Hide file tree

Showing 14 changed files with 152 additions and 87 deletions.
diff --git a/.maint/CONTRIBUTORS.md b/.maint/CONTRIBUTORS.md
@@ -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                                                                                                      |

diff --git a/.zenodo.json b/.zenodo.json
@@ -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",
@@ -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.",
@@ -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"
     },
     {
@@ -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"
     },
     {
@@ -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"
     },
     {
@@ -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",
@@ -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",
@@ -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",
@@ -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",
@@ -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.",

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,4 +1,4 @@
-23.2.0 (To be determined)
+23.2.0 (January 10, 2024)
 =========================
 New feature release in the 23.2.x series.
 
@@ -33,17 +33,27 @@ This release resolves a number of issues with fieldmaps inducing distortions
 during correction. Phase difference and direct fieldmaps are now masked correctly,
 preventing the overestimation of distortions outside the brain. Additionally,
 we now implement Jacobian weighting during unwarping, which corrects for compression
-and expansion effects on signal intensity.
+and expansion effects on signal intensity. To disable Jacobian weighting, use
+``--ignore fmap-jacobian``.
 
 Finally, a new resampling method has been added, to better account for
 susceptibility distortion and motion in a single shot resampling to a volumetric
 target space. We anticipate extending this to surface targets in the future.
 
+* FIX: Restore --ignore sbref functionality (#3180)
+* FIX: Retrieve atlas ROIs at requested density (#3179)
+* FIX: Keep minctracc executable in FreeSurfer installation (#3175)
+* FIX: Exclude echo entity from optimally combined derivatives (#3166)
+* FIX: Disable boldref-space outputs unless requested (#3159)
+* FIX: Tag memory estimates in resamplers (#3150)
 * FIX: Final revisions for next branch (#3134)
 * FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (#3098)
 * FIX: Connect EPI-to-fieldmap transform (#3099)
 * FIX: Use Py2-compatible version file template for fmriprep-docker (#3101)
 * FIX: Update connections to unwarp_wf, convert ITK transforms to text (#3077)
+* ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction (#3186)
+* ENH: Exclude non-steady-state volumes from confound correlation plot (#3171)
+* ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate (#3146)
 * ENH: Restore carpetplot and other final adjustments (#3131)
 * ENH: Restore CIFTI-2 generation (#3129)
 * ENH: Restore resampling to surface GIFTIs (#3126)
@@ -53,13 +63,25 @@ target space. We anticipate extending this to surface targets in the future.
 * ENH: Add MSMSulc (#3085)
 * ENH: Add reporting workflow for BOLD fit (#3082)
 * ENH: Generate anatomical derivatives useful for resampling (#3081)
+* RF: Load reportlets interfaces from nireports rather than niworkflows (#3176, #3184)
+* RF: Separate goodvoxels mask creation from fsLR resampling (#3170)
 * RF: Write out anatomical template derivatives (#3136)
 * RF: Update primary bold workflow to incorporate single shot resampling (#3114)
 * RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (#3078)
 * RF: Split fMRIPrep into fit and derivatives workflows (#2913)
+* RPT: Rename CSF/WM confounds in fMRIPlot (#3172)
+* TST: Add smoke tests for full workflow and most branching flags (#3155)
+* TST: Add smoke-tests for bold_fit_wf (#3152)
 * DOC: Fix documentation and description for init_bold_grayords_wf (#3051)
+* DOC: Minor updates in outputs.rst (#3148)
+* STY: Apply a couple refurb suggestions (#3151)
 * STY: Fix flake8 warnings (#3044)
 * STY: Apply pyupgrade suggestions (#3043)
+* MNT: Restore mritotal subcommands to Dockerfile (#3149)
+* MNT: Update smriprep to 0.13.1 (#3153)
+* MNT: optimise size of PNG files (#3145)
+* MNT: update vendored docs script ``github_link.py`` (#3144)
+* MNT: Update tedana pin, test on Python 3.12 (#3141)
 * MNT: Bump environment (#3132)
 * MNT: Bump version requirements (#3107)
 * MNT: http:// → https:// (#3097)
@@ -71,6 +93,7 @@ target space. We anticipate extending this to surface targets in the future.
 * MNT: update update_zenodo.py script (#3042)
 * MNT: Fix welcome message formatting and instructions (#3039)
 * MNT: Python 3.11 should be supported (#3038)
+* CI: Bump actions/setup-python from 4 to 5 (#3181)
 * CI: Stop testing legacy layout (#3079)
 * CI: Improve tag detection for docker builds (#3066)
 * CI: Clean up pre-release builds (#3040)

diff --git a/docs/outputs.rst b/docs/outputs.rst
@@ -484,7 +484,7 @@ Averaged value of confound (for example, mean ``framewise_displacement``)
 can also be added as regressors in group level analysis [Yan2013]_.
 *Regressors of motion spikes* for outlier censoring are generated from within *fMRIPrep*,
 and their calculation may be adjusted with the command line options ``--fd-spike-threshold``
-and ``--dvars-spike-threshold`` (defaults are FD > 0.5 mm or DVARS > 1.5).
+and ``--dvars-spike-threshold`` (defaults are FD > 0.5 mm or standardized DVARS > 1.5).
 Regressors of motion spikes are stored in separate ``motion_outlier_XX`` columns.
 
 **Discrete cosine-basis regressors**.

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
@@ -285,7 +285,7 @@ def _slice_time_ref(value, parser):
         action="store",
         nargs="+",
         default=[],
-        choices=["fieldmaps", "slicetiming", "sbref", "t2w", "flair"],
+        choices=["fieldmaps", "slicetiming", "sbref", "t2w", "flair", "fmap-jacobian"],
         help="Ignore selected aspects of the input dataset to disable corresponding "
         "parts of the workflow (a space delimited list)",
     )

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
@@ -229,12 +229,19 @@ def main():
         write_derivative_description(config.execution.bids_dir, config.execution.fmriprep_dir)
         write_bidsignore(config.execution.fmriprep_dir)
 
+        if failed_reports:
+            config.loggers.cli.error(
+                "Report generation was not successful for the following participants : %s.",
+                ", ".join(failed_reports),
+            )
+
         if sentry_sdk is not None and failed_reports:
             sentry_sdk.capture_message(
-                "Report generation failed for %d subjects" % failed_reports,
+                "Report generation was not successful for the following participants : %s.",
+                ", ".join(failed_reports),
                 level="error",
             )
-        sys.exit(int((errno + failed_reports) > 0))
+        sys.exit(int((errno + len(failed_reports)) > 0))
 
 
 if __name__ == "__main__":

diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
@@ -86,7 +86,6 @@ def build_workflow(config_file, retval):
     # Called with reports only
     if config.execution.reports_only:
         build_log.log(25, "Running --reports-only on participants %s", ", ".join(subject_list))
-
         session_list = (
             config.execution.bids_filters["bold"]["session"]
             if config.execution.bids_filters
@@ -95,12 +94,19 @@ def build_workflow(config_file, retval):
         if not isinstance(session_list, list):
             session_list = [session_list]
 
-        retval["return_code"] = generate_reports(
+        failed_reports = generate_reports(
             config.execution.participant_label,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
             session_list=session_list,
         )
+        if failed_reports:
+            config.loggers.cli.error(
+                "Report generation was not successful for the following participants : %s.",
+                ", ".join(failed_reports),
+            )
+
+        retval["return_code"] = len(failed_reports)
         return retval
 
     # Build main workflow