Merge pull request #2698 from nipreps/rel/21.0.1

REL: 21.0.1
nipreps · Jan 24, 2022 · 006c2a7 · 006c2a7
2 parents 5d4bf1f + d41c83c
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diff --git a/.mailmap b/.mailmap
@@ -9,6 +9,7 @@ Basile Pinsard <[email protected]> basile <[email protected]>
 Basile Pinsard <[email protected]> <[email protected]>
 Blaise Frederick <[email protected]>
 Blaise Frederick <[email protected]> bbfrederick <[email protected]>
+Celine Provins <[email protected]>
 Christopher J. Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
@@ -64,5 +65,6 @@ Sebastian Urchs <[email protected]>
 Sebastien Naze <[email protected]>
 Shoshana Berleant <[email protected]>  <[email protected]>
 Soichi Hayashi <[email protected]>
+Theo A.J. Schaefer <[email protected]>
 William Hedley Thompson <[email protected]>
 William Hedley Thompson <[email protected]> <[email protected]>
diff --git a/.zenodo.json b/.zenodo.json
@@ -2,6 +2,12 @@
   "title": "fMRIPrep: a robust preprocessing pipeline for functional MRI",
   "description": "<p>fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.</p>",
   "contributors": [
+    {
+      "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne",
+      "name": "Provins, C\u00e9line",
+      "orcid": "0000-0002-1668-9629",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toru\u0144",
       "name": "Finc, Karolina",
@@ -32,6 +38,18 @@
       "orcid": "0000-0002-2365-8265",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957",
+      "type": "Researcher"
+    },
+    {
+      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
+      "name": "Schaefer, Theo A.J.",
+      "orcid": "0000-0003-4102-559X",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Montreal Neurological Institute, McGill University",
       "name": "Urchs, Sebastian",
@@ -50,18 +68,18 @@
       "orcid": "0000-0002-2050-0614",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Department of Psychology, Columbia University",
-      "name": "Jacoby, Nir",
-      "orcid": "0000-0001-7936-9991",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
       "name": "Mentch, Jeff",
       "orcid": "0000-0002-7762-8678",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Department of Psychology, Columbia University",
+      "name": "Jacoby, Nir",
+      "orcid": "0000-0001-7936-9991",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Department of Radiology, Weill Cornell Medicine",
       "name": "Jamison, Keith W.",
@@ -98,6 +116,12 @@
       "orcid": "0000-0001-6424-8740",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
+      "name": "Nitsch, Alexander",
+      "orcid": "0000-0002-5740-9451",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Ma, Feilong",
@@ -176,12 +200,6 @@
       "orcid": "0000-0001-6948-9068",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne",
-      "name": "Provins, C\u00e9line",
-      "orcid": "0000-0002-1668-9629",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Neuroscience Program, University of Iowa",
       "name": "Rivera-Dompenciel, Adriana",
@@ -218,12 +236,6 @@
       "orcid": "0000-0002-5749-6049",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
-      "name": "Waller, Lea",
-      "orcid": "0000-0002-3239-6957",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Wright, Jessey",
@@ -241,18 +253,6 @@
       "name": "Ghosh, Satrajit S.",
       "orcid": "0000-0002-5312-6729",
       "type": "Researcher"
-    },
-    {
-      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
-      "name": "Schaefer, Theo A.J.",
-      "orcid": "0000-0003-4102-559X",
-      "type": "Researcher"
-    },
-    {
-      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
-      "name": "Nitsch, Alexander",
-      "orcid": "0000-0002-5740-9451",
-      "type": "Researcher"
     }
   ],
   "creators": [
@@ -271,26 +271,26 @@
       "name": "Goncalves, Mathias",
       "orcid": "0000-0002-7252-7771"
     },
-    {
-      "affiliation": "Montreal Neurological Institute, McGill University",
-      "name": "DuPre, Elizabeth",
-      "orcid": "0000-0003-1358-196X"
-    },
     {
       "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",
       "name": "Ciric, Rastko",
       "orcid": "0000-0001-6347-7939"
     },
+    {
+      "affiliation": "Department of Psychology, Florida International University",
+      "name": "Salo, Taylor",
+      "orcid": "0000-0001-9813-3167"
+    },
     {
       "affiliation": "SIMEXP Lab, CRIUGM, University of Montr\u00e9al, Montr\u00e9al, Canada",
       "name": "Pinsard, Basile",

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,16 +1,45 @@
+21.0.1 (January 24, 2022)
+=========================
+Bug-fix release in the 21.0.x series.
+
+This release re-enables reverse-PE EPI fieldmaps, i.e. EPIs acquired with the
+opposite phase-encoding direction to a BOLD series.
+Additionally, the ``--use-syn-sdc`` option will now error by default if no
+``PhaseEncodingDirection`` can be found for a BOLD series. To reduce this to
+a warning, use ``--use-syn-sdc warn``. SyN-SDC will NOT be run, but the workflow
+will proceed.
+
+.. note::
+
+  ``topup`` runtime scales with the number of volumes used, so fMRIPrep defaults to
+  using a maximum of 5 volumes from each of the BOLD series and the EPI fieldmap.
+  To adjust this, please use the ``--topup-max-vols`` parameter.
+
+* FIX: Create single fmap_select_std node for use with all ANAT estimators (#2692)
+* FIX: Re-enable reverse-PE EPI fieldmaps (#2684)
+* FIX: Pass boolean use_syn_sdc to find_estimators (#2685)
+* FIX: Ensure AROMA inputs are uncompressed if --low-mem (#2657)
+* ENH: Add ``--topup-max-vols`` flag to control TOPUP runtime (#2688)
+* ENH: Allow ``--use-syn-sdc`` to take a "warn" option to avoid exiting when PE dir is unavailable (#2680)
+* RF: Add extension field to differentiate from upcoming templates (#2613)
+* WRAPPER: Map ``--bids-filter-file``\s into Docker container (#2691)
+* MNT: Silence warning from pybids; list packaging as dependency (#2689)
+* MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)
+* MNT: Restore nitime to requirements, necessary for DVARS (#2678)
+
 21.0.0 (December 14, 2021)
 ==========================
 A new series is finally here!
 
 Some highlights of this version's new features include a substantial rework of fMRIPrep's
-susceptibility distortion correction (including the addition of FSL's `topup` as the new
+susceptibility distortion correction (including the addition of FSL's ``topup`` as the new
 default PEPOLAR correction technique), improved flexibility for multiecho scans, and
 dependency version upgrades within the Docker environment.
 
 .. note::
 
   To follow BIDS Derivatives more closely, *fMRIPrep*'s default output layout has changed.
-  To enable the legacy layout, use the `--output-layout legacy` flag.
+  To enable the legacy layout, use the ``--output-layout legacy`` flag.
   For more information, please see https://fmriprep.org/en/latest/outputs.html#layout
 
 .. caution::
@@ -27,7 +56,7 @@ A full list of changes can be found below.
 * DOC: Remove mention to ``epidewarp.fsl`` from ``NOTICE`` (#2629)
 * DOC: Update description of output layout, add discussion of legacy mode (#2646)
 * DOC: ME | Add missing output to documentation, improve boilerplate (#2608)
-* DOC: Add --index-metadata to `pybids layout` faq (#2546)
+* DOC: Add --index-metadata to ``pybids layout`` faq (#2546)
 * DOC: Add warning about slice timing correction in output documentation. (#2502)
 * DOC: Update sample report (#2519)
 * DOC: Refactor README and citing information (#2474)

diff --git a/setup.cfg b/setup.cfg
@@ -33,7 +33,7 @@ install_requires =
     psutil >= 5.4
     pybids >= 0.12.1
     requests
-    sdcflows ~= 2.0.9
+    sdcflows ~= 2.0.11
     smriprep ~= 0.8.0
     tedana ~= 0.0.9
     templateflow >= 0.6