From 9f7278685a05dad7f3406bc8c8af8dd98f2f840b Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 9 Sep 2021 08:41:58 -0400
Subject: [PATCH 01/21] FIX: Restore SyN-SDC

---
 fmriprep/workflows/base.py | 56 ++++++++++++++++++++++++++++++++------
 1 file changed, 47 insertions(+), 9 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index c209426f0..7abfa970f 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -312,11 +312,10 @@ def init_single_subject_wf(subject_id):
         return workflow
 
     fmap_estimators = None
-    # TODO 21.0.0: Implement SyN
-    if any((config.workflow.use_syn_sdc, config.workflow.force_syn)):
-        config.loggers.workflow.critical("SyN processing is not yet implemented.")
 
-    if "fieldmaps" not in config.workflow.ignore:
+    if any(("fieldmaps" not in config.workflow.ignore,
+            config.workflow.use_syn_sdc,
+            config.workflow.force_syn)):
         from sdcflows.utils.wrangler import find_estimators
 
         # SDC Step 1: Run basic heuristics to identify available data for fieldmap estimation
@@ -324,8 +323,8 @@ def init_single_subject_wf(subject_id):
         fmap_estimators = find_estimators(
             layout=config.execution.layout,
             subject=subject_id,
-            fmapless=False,  # config.workflow.use_syn_sdc,
-            force_fmapless=False,  # config.workflow.force_syn,
+            fmapless=config.workflow.use_syn_sdc,
+            force_fmapless=config.workflow.force_syn,
         )
 
         config.loggers.workflow.debug(
@@ -333,6 +332,14 @@ def init_single_subject_wf(subject_id):
             f"{[e.method for e in fmap_estimators]}"
         )
 
+        if "fieldmaps" in config.workflow.ignore:
+            fmap_estimators = [f for f in fmap_estimators
+                               if f.method == fm.EstimatorType.ANAT]
+            config.loggers.workflow.debug(
+                "Ignoring fieldmap scans, using anatomical estimators: "
+                f"{[e.method for e in fmap_estimators]}"
+            )
+
     # Append the functional section to the existing anatomical exerpt
     # That way we do not need to stream down the number of bold datasets
     anat_preproc_wf.__postdesc__ = (anat_preproc_wf.__postdesc__ or '') + """
@@ -424,13 +431,44 @@ def init_single_subject_wf(subject_id):
             getattr(fmap_wf.inputs, f"in_{estimator.bids_id}").metadata = [
                 s.metadata for s in estimator.sources
             ]
-            continue
 
-        if estimator.method == fm.EstimatorType.PEPOLAR:
+        elif estimator.method == fm.EstimatorType.PEPOLAR:
             raise NotImplementedError(
                 "Sophisticated PEPOLAR schemes are unsupported."
             )
-        # TODO: SyN fieldmap processing
+
+        elif estimator.method == fm.EstimatorType.ANAT:
+            from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
+            sources = [str(s.path) for s in estimator.sources if s.suffix == "bold"]
+            layout = config.execution.layout
+            syn_preprocessing_wf = init_syn_preprocessing_wf(
+                omp_nthreads=config.nipype.omp_nthreads,
+                debug=config.execution.sloppy,
+                auto_bold_nss=True,
+                t1w_inversion=True,
+                name=f"syn_preprocessing_{estimator.bids_ids}",
+            )
+            syn_preprocessing_wf.inputs.inputnode.in_epis = sources
+            syn_preprocessing_wf.inputs.inputnode.in_meta = [
+                layout.get_metadata(s) for s in sources
+            ]
+
+            # fmt:off
+            workflow.connect([
+                (anat_preproc_wf, syn_preprocessing_wf, [
+                    ("outputnode.t1w_preproc", "inputnode.in_anat"),
+                    ("outputnode.t1w_mask", "inputnode.mask_anat"),
+                    ("outputnode.std2anat_xfm", "inputnode.std2anat_xfm"),
+                ]),
+                (syn_preprocessing_wf, fmap_wf, [
+                    ("outputnode.epi_ref", f"in_{estimator.bids_id}.epi_ref"),
+                    ("outputnode.epi_mask", f"in_{estimator.bids_id}.epi_mask"),
+                    ("outputnode.anat_ref", f"in_{estimator.bids_id}.anat_ref"),
+                    ("outputnode.anat_mask", f"in_{estimator.bids_id}.anat_mask"),
+                    ("outputnode.sd_prior", f"in_{estimator.bids_id}.sd_prior"),
+                ]),
+            ])
+            # fmt:on
 
     return workflow
 

From 52f7eb5a6bee50d8c5bb8349b38540d3327b2081 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 10 Sep 2021 13:01:24 -0400
Subject: [PATCH 02/21] FIX: Make sure variables exist before referencing

---
 fmriprep/workflows/base.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 7abfa970f..47643ac7d 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -311,6 +311,7 @@ def init_single_subject_wf(subject_id):
     if anat_only:
         return workflow
 
+    from sdcflows import fieldmaps as fm
     fmap_estimators = None
 
     if any(("fieldmaps" not in config.workflow.ignore,
@@ -380,7 +381,6 @@ def init_single_subject_wf(subject_id):
         return workflow
 
     from sdcflows.workflows.base import init_fmap_preproc_wf
-    from sdcflows import fieldmaps as fm
 
     fmap_wf = init_fmap_preproc_wf(
         debug="fieldmaps" in config.execution.debug,
@@ -446,7 +446,7 @@ def init_single_subject_wf(subject_id):
                 debug=config.execution.sloppy,
                 auto_bold_nss=True,
                 t1w_inversion=True,
-                name=f"syn_preprocessing_{estimator.bids_ids}",
+                name=f"syn_preprocessing_{estimator.bids_id}",
             )
             syn_preprocessing_wf.inputs.inputnode.in_epis = sources
             syn_preprocessing_wf.inputs.inputnode.in_meta = [

From fbc8b90d865ffffab2f526e2f6bb576c38b8da9d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 10 Sep 2021 16:21:52 -0400
Subject: [PATCH 03/21] FIX: Pass imputed metadata to syn_preprocessing and
 unwarp

---
 fmriprep/workflows/base.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 47643ac7d..f68adf4cf 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -440,7 +440,7 @@ def init_single_subject_wf(subject_id):
         elif estimator.method == fm.EstimatorType.ANAT:
             from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
             sources = [str(s.path) for s in estimator.sources if s.suffix == "bold"]
-            layout = config.execution.layout
+            source_meta = [s.metadata for s in estimator.sources if s.suffix == "bold"]
             syn_preprocessing_wf = init_syn_preprocessing_wf(
                 omp_nthreads=config.nipype.omp_nthreads,
                 debug=config.execution.sloppy,
@@ -449,9 +449,7 @@ def init_single_subject_wf(subject_id):
                 name=f"syn_preprocessing_{estimator.bids_id}",
             )
             syn_preprocessing_wf.inputs.inputnode.in_epis = sources
-            syn_preprocessing_wf.inputs.inputnode.in_meta = [
-                layout.get_metadata(s) for s in sources
-            ]
+            syn_preprocessing_wf.inputs.inputnode.in_meta = source_meta
 
             # fmt:off
             workflow.connect([
@@ -470,6 +468,14 @@ def init_single_subject_wf(subject_id):
             ])
             # fmt:on
 
+            # TotalReadoutTime is calculated or imputed by find_estimators
+            # Use enhanced metadata for SyN-SDC
+            from .bold.base import _get_wf_name
+            for func_preproc_wf in func_preproc_wfs:
+                for source, meta in zip(sources, source_meta):
+                    if func_preproc_wf.name == _get_wf_name(source):
+                        func_preproc_wf.inputs.unwarp_wf.inputnode.metadata = meta
+
     return workflow
 
 

From 5936720c386e36045de80b22d1b1875370b9426a Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 14 Sep 2021 14:44:36 -0400
Subject: [PATCH 04/21] ENH: Fail if SyN is requested but cannot be run

---
 fmriprep/workflows/base.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index f68adf4cf..f2016da18 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -328,6 +328,13 @@ def init_single_subject_wf(subject_id):
             force_fmapless=config.workflow.force_syn,
         )
 
+        if config.workflow.use_syn_sdc and not fmap_estimators:
+            message = ("Fieldmap-less (SyN) estimation was requested, but "
+                       "PhaseEncodingDirection information appears to be "
+                       "absent.")
+            config.loggers.workflow.error(message)
+            raise ValueError(message)
+
         config.loggers.workflow.debug(
             f"{len(fmap_estimators)} fieldmap estimators found: "
             f"{[e.method for e in fmap_estimators]}"

From f9f9c8578efc464f5ac9aeec91a4f357c72689a3 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 15 Sep 2021 17:34:56 +0200
Subject: [PATCH 05/21] enh: update workflows to account for new resampling

**multi-echo not yet covered!!!!**
---
 fmriprep/workflows/bold/base.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index d0af5772c..8ebac9707 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -1101,7 +1101,6 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             (("outputnode.fieldwarp", _pop), "inputnode.fieldwarp"),
         ]),
         (unwarp_wf, bold_final, [("outputnode.corrected", "bold")]),
-
     ])
     # fmt:on
 

From a4878e237dc89e5a38bf4fa10e22fb9de07baddc Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Thu, 23 Sep 2021 11:27:45 +0200
Subject: [PATCH 06/21] pin: sdcflows on feature branch

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 1a7e8ae3f..86ddca685 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -31,7 +31,7 @@ install_requires =
     psutil >= 5.4
     pybids >= 0.12.1
     requests
-    sdcflows @ git+https://github.com/nipreps/sdcflows.git@master
+    sdcflows @ git+https://github.com/nipreps/sdcflows.git@fix/syn-revision
     smriprep ~= 0.8.0
     tedana ~= 0.0.9
     templateflow >= 0.6

From 51dfcb2f61492ab025903c2c37c124b54680527c Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 1 Oct 2021 10:33:05 +0200
Subject: [PATCH 07/21] fix: fieldmapless tripped when several std spaces are
 available

---
 fmriprep/workflows/base.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index f2016da18..58f24db39 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -445,7 +445,9 @@ def init_single_subject_wf(subject_id):
             )
 
         elif estimator.method == fm.EstimatorType.ANAT:
+            from niworkflows.interfaces.utility import KeySelect
             from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
+
             sources = [str(s.path) for s in estimator.sources if s.suffix == "bold"]
             source_meta = [s.metadata for s in estimator.sources if s.suffix == "bold"]
             syn_preprocessing_wf = init_syn_preprocessing_wf(
@@ -458,12 +460,24 @@ def init_single_subject_wf(subject_id):
             syn_preprocessing_wf.inputs.inputnode.in_epis = sources
             syn_preprocessing_wf.inputs.inputnode.in_meta = source_meta
 
+            # Select "MNI152NLin2009cAsym" from standard references.
+            fmap_select_std = pe.Node(
+                KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"),
+                name="fmap_select_std",
+                run_without_submitting=True,
+            )
+
             # fmt:off
             workflow.connect([
+                (anat_preproc_wf, fmap_select_std, [
+                    ("outputnode.std2anat_xfm", "std2anat_xfm"),
+                    ("outputnode.template", "keys")]),
                 (anat_preproc_wf, syn_preprocessing_wf, [
                     ("outputnode.t1w_preproc", "inputnode.in_anat"),
                     ("outputnode.t1w_mask", "inputnode.mask_anat"),
-                    ("outputnode.std2anat_xfm", "inputnode.std2anat_xfm"),
+                ]),
+                (fmap_select_std, syn_preprocessing_wf, [
+                    ("std2anat_xfm", "inputnode.std2anat_xfm"),
                 ]),
                 (syn_preprocessing_wf, fmap_wf, [
                     ("outputnode.epi_ref", f"in_{estimator.bids_id}.epi_ref"),

From 5a922d1270f0158ffc4eef7485fbd1981acdbea4 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 6 Oct 2021 16:57:44 +0200
Subject: [PATCH 08/21] enh: better integration of *SDCFlows*' unwarping

This PR builds on top of #2547, unifying the final BOLDref computation.
---
 fmriprep/workflows/bold/base.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 8ebac9707..acf68961a 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -628,6 +628,9 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             (inputnode, func_derivatives_wf, [("bold_file", "inputnode.source_file")]),
             (bold_split, bold_t1_trans_wf, [("out_files", "inputnode.bold_split")]),
             (bold_hmc_wf, bold_t1_trans_wf, [("outputnode.xforms", "inputnode.hmc_xforms")]),
+            (final_boldref_wf, bold_final, [
+                ("outputnode.ref_image", "boldref"),
+            ]),
         ])
         # fmt:on
     else:  # for meepi, use optimal combination

From 49ca92a08e6183c67efe7ca9108c9a56fba31d05 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 6 Oct 2021 19:12:13 +0200
Subject: [PATCH 09/21] enh: remove unnecessary setting

---
 fmriprep/workflows/base.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 58f24db39..073b64523 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -488,15 +488,6 @@ def init_single_subject_wf(subject_id):
                 ]),
             ])
             # fmt:on
-
-            # TotalReadoutTime is calculated or imputed by find_estimators
-            # Use enhanced metadata for SyN-SDC
-            from .bold.base import _get_wf_name
-            for func_preproc_wf in func_preproc_wfs:
-                for source, meta in zip(sources, source_meta):
-                    if func_preproc_wf.name == _get_wf_name(source):
-                        func_preproc_wf.inputs.unwarp_wf.inputnode.metadata = meta
-
     return workflow
 
 

From a3bab644d6647e1121525a9c1f536088d496c5e0 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Thu, 7 Oct 2021 15:36:17 +0200
Subject: [PATCH 10/21] fix: sloppy merge with master

---
 fmriprep/workflows/bold/base.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index acf68961a..8ebac9707 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -628,9 +628,6 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             (inputnode, func_derivatives_wf, [("bold_file", "inputnode.source_file")]),
             (bold_split, bold_t1_trans_wf, [("out_files", "inputnode.bold_split")]),
             (bold_hmc_wf, bold_t1_trans_wf, [("outputnode.xforms", "inputnode.hmc_xforms")]),
-            (final_boldref_wf, bold_final, [
-                ("outputnode.ref_image", "boldref"),
-            ]),
         ])
         # fmt:on
     else:  # for meepi, use optimal combination

From 5b3b39dd5f5c55bec4f9bc6a6e69567b589e3e50 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Thu, 7 Oct 2021 15:37:54 +0200
Subject: [PATCH 11/21] maint: update sdcflows dependency link pin

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 86ddca685..1a7e8ae3f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -31,7 +31,7 @@ install_requires =
     psutil >= 5.4
     pybids >= 0.12.1
     requests
-    sdcflows @ git+https://github.com/nipreps/sdcflows.git@fix/syn-revision
+    sdcflows @ git+https://github.com/nipreps/sdcflows.git@master
     smriprep ~= 0.8.0
     tedana ~= 0.0.9
     templateflow >= 0.6

From 60f17b22359654ae96f8b99934dd504e02e5fab4 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 18 Oct 2021 21:25:43 +0200
Subject: [PATCH 12/21] fix: set T1w inversion flag to ``False``

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Mathias Goncalves <mathiasg@stanford.edu>
---
 fmriprep/workflows/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 073b64523..7d0553b95 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -454,7 +454,7 @@ def init_single_subject_wf(subject_id):
                 omp_nthreads=config.nipype.omp_nthreads,
                 debug=config.execution.sloppy,
                 auto_bold_nss=True,
-                t1w_inversion=True,
+                t1w_inversion=False,
                 name=f"syn_preprocessing_{estimator.bids_id}",
             )
             syn_preprocessing_wf.inputs.inputnode.in_epis = sources

From 9de0ac68397abf3c92f5e8c6085f27f7afc61099 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 18 Oct 2021 21:49:19 +0200
Subject: [PATCH 13/21] enh: inject pretend PE metadata in CircleCI tests

---
 .circleci/config.yml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 00ebd7c58..e61d756cb 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -478,6 +478,12 @@ jobs:
          paths:
             - /tmp/ds005/work
 
+      - run:
+          name: Attempt run without PE metadata (should fail)
+          no_output_timeout: 2h
+          command: |
+            echo "TODO"
+
       - run:
           name: Run full fMRIPrep on ds005 (LegacyMultiProc plugin)
           no_output_timeout: 2h
@@ -486,6 +492,15 @@ jobs:
             if [ -f /tmp/.nofasttrack ]; then
                 FASTRACK_ARG=""
             fi
+
+            # Inject pretend metadata
+            echo '{"PhaseEncodingDirection": "j"}' >> /tmp/data/${DATASET}/bold.json
+
+            # REMOVE in case the above works out
+            # json_sidecar=/tmp/data/${DATASET}/task-mixedgamblestask_bold.json
+            # awk 'NR==1{print; print "    \"TotalReadoutTime\": 0.05,"} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
+            # awk 'NR==1{print; print "    \"PhaseEncodingDirection\": \"j\","} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
+
             fmriprep-docker -i nipreps/fmriprep:latest \
                 -e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
                 --network none \
@@ -879,6 +894,12 @@ jobs:
          paths:
             - /tmp/ds210/work
 
+      - run:
+          name: Attempt run without PE metadata (should fail)
+          no_output_timeout: 2h
+          command: |
+            echo "TODO"
+
       - run:
           name: Run full fMRIPrep on ds000210
           no_output_timeout: 2h
@@ -887,6 +908,11 @@ jobs:
             if [ -f /tmp/.nofasttrack ]; then
                 FASTRACK_ARG=""
             fi
+
+            # Inject pretend metadata for SDCFlows not to crash
+            # TODO / open question - do all echos need the metadata?
+            echo '{"PhaseEncodingDirection": "j"}' >> /tmp/data/${DATASET}/task-cuedSGT_bold.json
+
             fmriprep-docker -i nipreps/fmriprep:latest \
                 -e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
                 --config $PWD/nipype.cfg -w /tmp/${DATASET}/work \

From 283a3d5ffb272a406076174f9d500158bbd09f25 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 18 Oct 2021 22:50:39 +0200
Subject: [PATCH 14/21] fix: circleci tests failed for spurious reasons

---
 .circleci/config.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e61d756cb..2c88ec50b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -494,12 +494,9 @@ jobs:
             fi
 
             # Inject pretend metadata
-            echo '{"PhaseEncodingDirection": "j"}' >> /tmp/data/${DATASET}/bold.json
-
-            # REMOVE in case the above works out
-            # json_sidecar=/tmp/data/${DATASET}/task-mixedgamblestask_bold.json
-            # awk 'NR==1{print; print "    \"TotalReadoutTime\": 0.05,"} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
-            # awk 'NR==1{print; print "    \"PhaseEncodingDirection\": \"j\","} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
+            json_sidecar=/tmp/data/${DATASET}/task-mixedgamblestask_bold.json
+            awk 'NR==1{print; print "    \"TotalReadoutTime\": 0.05,"} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
+            awk 'NR==1{print; print "    \"PhaseEncodingDirection\": \"j\","} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
 
             fmriprep-docker -i nipreps/fmriprep:latest \
                 -e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
@@ -911,7 +908,9 @@ jobs:
 
             # Inject pretend metadata for SDCFlows not to crash
             # TODO / open question - do all echos need the metadata?
+            chmod +w /tmp/data/${DATASET}
             echo '{"PhaseEncodingDirection": "j"}' >> /tmp/data/${DATASET}/task-cuedSGT_bold.json
+            chmod -R -w /tmp/data/${DATASET}
 
             fmriprep-docker -i nipreps/fmriprep:latest \
                 -e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \

From b2c27ab60fee12b8ed5f21c301d77a5f727e1bba Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 19 Oct 2021 09:39:56 +0200
Subject: [PATCH 15/21] fix: update ds005's ouputs listings with new outputs

---
 .circleci/ds005_bids_fasttrack_outputs.txt           | 6 ++++++
 .circleci/ds005_bids_outputs.txt                     | 6 ++++++
 .circleci/ds005_legacy_fasttrack_outputs.txt         | 6 ++++++
 .circleci/ds005_legacy_outputs.txt                   | 6 ++++++
 .circleci/ds005_legacy_partial_fasttrack_outputs.txt | 6 ++++++
 .circleci/ds005_legacy_partial_outputs.txt           | 6 ++++++
 6 files changed, 36 insertions(+)

diff --git a/.circleci/ds005_bids_fasttrack_outputs.txt b/.circleci/ds005_bids_fasttrack_outputs.txt
index f45fd93ac..5a6a8e982 100644
--- a/.circleci/ds005_bids_fasttrack_outputs.txt
+++ b/.circleci/ds005_bids_fasttrack_outputs.txt
@@ -9,6 +9,12 @@ bids/logs/CITATION.html
 bids/logs/CITATION.md
 bids/logs/CITATION.tex
 bids/sub-01
+bids/sub-01/fmap
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 bids/sub-01/func
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.tsv
diff --git a/.circleci/ds005_bids_outputs.txt b/.circleci/ds005_bids_outputs.txt
index ac4d943ce..c7db60bcd 100644
--- a/.circleci/ds005_bids_outputs.txt
+++ b/.circleci/ds005_bids_outputs.txt
@@ -40,6 +40,12 @@ bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
 bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
+bids/sub-01/fmap
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
+bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 bids/sub-01/func
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.tsv
diff --git a/.circleci/ds005_legacy_fasttrack_outputs.txt b/.circleci/ds005_legacy_fasttrack_outputs.txt
index 8ba8bfd88..9f1db0804 100644
--- a/.circleci/ds005_legacy_fasttrack_outputs.txt
+++ b/.circleci/ds005_legacy_fasttrack_outputs.txt
@@ -9,6 +9,12 @@ fmriprep/logs/CITATION.html
 fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-01
+fmriprep/sub-01/fmap
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
diff --git a/.circleci/ds005_legacy_outputs.txt b/.circleci/ds005_legacy_outputs.txt
index 18016f826..82901dc59 100644
--- a/.circleci/ds005_legacy_outputs.txt
+++ b/.circleci/ds005_legacy_outputs.txt
@@ -50,6 +50,12 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_dseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
+fmriprep/sub-01/fmap
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
diff --git a/.circleci/ds005_legacy_partial_fasttrack_outputs.txt b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt
index 65e965a78..095256f05 100644
--- a/.circleci/ds005_legacy_partial_fasttrack_outputs.txt
+++ b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt
@@ -9,6 +9,12 @@ fmriprep/logs/CITATION.html
 fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-01
+fmriprep/sub-01/fmap
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
diff --git a/.circleci/ds005_legacy_partial_outputs.txt b/.circleci/ds005_legacy_partial_outputs.txt
index 6456fc15f..c98d4e6c7 100644
--- a/.circleci/ds005_legacy_partial_outputs.txt
+++ b/.circleci/ds005_legacy_partial_outputs.txt
@@ -50,6 +50,12 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_dseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
+fmriprep/sub-01/fmap
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json

From 215770c100e4f7b59e1d1e783af83e4903d14346 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 19 Oct 2021 09:41:05 +0200
Subject: [PATCH 16/21] fix: update ds210's ouputs listings with new outputs

---
 .circleci/ds210_fasttrack_outputs.txt | 6 ++++++
 .circleci/ds210_outputs.txt           | 6 ++++++
 2 files changed, 12 insertions(+)

diff --git a/.circleci/ds210_fasttrack_outputs.txt b/.circleci/ds210_fasttrack_outputs.txt
index d40943dc2..2704fc507 100644
--- a/.circleci/ds210_fasttrack_outputs.txt
+++ b/.circleci/ds210_fasttrack_outputs.txt
@@ -7,6 +7,12 @@ fmriprep/logs/CITATION.html
 fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-02
+fmriprep/sub-02/fmap
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-02/func
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.tsv
diff --git a/.circleci/ds210_outputs.txt b/.circleci/ds210_outputs.txt
index aa9ea6b18..b2a31e7bf 100644
--- a/.circleci/ds210_outputs.txt
+++ b/.circleci/ds210_outputs.txt
@@ -26,6 +26,12 @@ fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_dseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
+fmriprep/sub-02/fmap
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-02/fmap/sub-02_run-1_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-02/func
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.tsv

From 47c947d033c363e928ba5de3cbcd8530d670fe08 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 19 Oct 2021 12:01:28 +0200
Subject: [PATCH 17/21] fix: ensure the ME pathway does not crash at workflow
 build-time

---
 fmriprep/workflows/base.py      | 26 +++++++++++++++++---------
 fmriprep/workflows/bold/base.py | 12 ++++++++----
 2 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 7d0553b95..c45cca4b3 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -335,17 +335,23 @@ def init_single_subject_wf(subject_id):
             config.loggers.workflow.error(message)
             raise ValueError(message)
 
-        config.loggers.workflow.debug(
-            f"{len(fmap_estimators)} fieldmap estimators found: "
-            f"{[e.method for e in fmap_estimators]}"
-        )
-
-        if "fieldmaps" in config.workflow.ignore:
+        if (
+            "fieldmaps" in config.workflow.ignore
+            and [f for f in fmap_estimators
+                 if f.method != fm.EstimatorType.ANAT]
+        ):
+            config.loggers.workflow.info(
+                'Option "--ignore fieldmaps" was set, but either "--use-syn-sdc" '
+                'or "--force-syn" were given, so fieldmap-less estimation will be executed.'
+            )
             fmap_estimators = [f for f in fmap_estimators
                                if f.method == fm.EstimatorType.ANAT]
-            config.loggers.workflow.debug(
-                "Ignoring fieldmap scans, using anatomical estimators: "
-                f"{[e.method for e in fmap_estimators]}"
+
+        if fmap_estimators:
+            config.loggers.workflow.info(
+                "B0 field inhomogeneity map will be estimated with "
+                f" the following {len(fmap_estimators)} estimators: "
+                f"{[e.method for e in fmap_estimators]}."
             )
 
     # Append the functional section to the existing anatomical exerpt
@@ -426,6 +432,8 @@ def init_single_subject_wf(subject_id):
         config.loggers.workflow.info(f"""\
 Setting-up fieldmap "{estimator.bids_id}" ({estimator.method}) with \
 <{', '.join(s.path.name for s in estimator.sources)}>""")
+
+        # Mapped and phasediff can be connected internally by SDCFlows
         if estimator.method in (fm.EstimatorType.MAPPED, fm.EstimatorType.PHASEDIFF):
             continue
 
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 8ebac9707..246ca16c7 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -252,15 +252,19 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             from sdcflows.fieldmaps import get_identifier
 
             # Fallback to IntendedFor
-            bold_rel = re.sub(
-                r"^sub-[a-zA-Z0-9]*/", "", str(Path(bold_file).relative_to(layout.root))
+            intended_rel = re.sub(
+                r"^sub-[a-zA-Z0-9]*/",
+                "",
+                str(Path(
+                    bold_file if not multiecho else bold_file[0]
+                ).relative_to(layout.root))
             )
-            estimator_key = get_identifier(bold_rel)
+            estimator_key = get_identifier(intended_rel)
 
         if not estimator_key:
             has_fieldmap = False
             config.loggers.workflow.critical(
-                f"None of the available B0 fieldmaps are associated to <{bold_rel}>"
+                f"None of the available B0 fieldmaps are associated to <{bold_file}>"
             )
         else:
             config.loggers.workflow.info(f"Found usable B0 fieldmap <{estimator_key}>")

From dc45b4a9d78872cf5f8ff8f0c3dea1638eb767f6 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 20 Oct 2021 09:36:09 +0200
Subject: [PATCH 18/21] fix: errors in naming of ds005 outputs

---
 .circleci/ds005_legacy_partial_fasttrack_outputs.txt | 10 +++++-----
 .circleci/ds005_legacy_partial_outputs.txt           | 10 +++++-----
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.circleci/ds005_legacy_partial_fasttrack_outputs.txt b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt
index 095256f05..bdf7a0360 100644
--- a/.circleci/ds005_legacy_partial_fasttrack_outputs.txt
+++ b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt
@@ -10,11 +10,11 @@ fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/fmap
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
diff --git a/.circleci/ds005_legacy_partial_outputs.txt b/.circleci/ds005_legacy_partial_outputs.txt
index c98d4e6c7..0f60c597e 100644
--- a/.circleci/ds005_legacy_partial_outputs.txt
+++ b/.circleci/ds005_legacy_partial_outputs.txt
@@ -51,11 +51,11 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 fmriprep/sub-01/fmap
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
-fmriprep/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-preproc_fieldmap.json
+fmriprep/sub-01/fmap/sub-01_run-2_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json

From b9fbbdbf7533198d70ca363a6a305e4d8040d6fd Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 20 Oct 2021 09:36:31 +0200
Subject: [PATCH 19/21] fix: multi-echo + SDC wiring issue

---
 fmriprep/workflows/bold/base.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 246ca16c7..fb7defcd8 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -267,7 +267,9 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
                 f"None of the available B0 fieldmaps are associated to <{bold_file}>"
             )
         else:
-            config.loggers.workflow.info(f"Found usable B0 fieldmap <{estimator_key}>")
+            config.loggers.workflow.info(
+                f"Found usable B0-map (fieldmap) estimator(s) <{', '.join(estimator_key)}> "
+                f"to correct <{bold_file}> for susceptibility-derived distortions.")
 
     # Check whether STC must/can be run
     run_stc = (
@@ -644,9 +646,6 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             (join_echos, bold_t2s_wf, [("bold_files", "inputnode.bold_file")]),
             (bold_t2s_wf, split_opt_comb, [("outputnode.bold", "in_file")]),
             (split_opt_comb, bold_t1_trans_wf, [("out_files", "inputnode.bold_split")]),
-            (bold_t2s_wf, bold_final, [
-                ("outputnode.bold", "bold"),
-            ]),
         ])
         # fmt:on
 
@@ -1011,6 +1010,9 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
                 (bold_bold_trans_wf, bold_t2s_wf, [
                     (("outputnode.bold_mask", pop_file), "inputnode.bold_mask"),
                 ]),
+                (bold_t2s_wf, bold_final, [
+                    ("outputnode.bold", "bold"),
+                ]),
             ]
         )
         # fmt:on

From 5afadd3019cf051c9dab517017d93e64bf949193 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 22 Oct 2021 16:01:59 +0200
Subject: [PATCH 20/21] fix: address issue with metadata [skip ci]

---
 .circleci/config.yml            | 2 +-
 fmriprep/workflows/bold/base.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b8607e141..1c892b83d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -893,7 +893,7 @@ jobs:
             # Inject pretend metadata for SDCFlows not to crash
             # TODO / open question - do all echos need the metadata?
             chmod +w /tmp/data/${DATASET}
-            echo '{"PhaseEncodingDirection": "j"}' >> /tmp/data/${DATASET}/task-cuedSGT_bold.json
+            echo '{"PhaseEncodingDirection": "j", "TotalReadoutTime": 0.058}' >> /tmp/data/${DATASET}/task-cuedSGT_bold.json
             chmod -R -w /tmp/data/${DATASET}
 
             fmriprep-docker -i nipreps/fmriprep:latest \
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 0e0709e07..982485139 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -1035,7 +1035,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
         debug="fieldmaps" in config.execution.debug,
         omp_nthreads=config.nipype.omp_nthreads,
     )
-    unwarp_wf.inputs.inputnode.metadata = layout.get_metadata(str(bold_file))
+    unwarp_wf.inputs.inputnode.metadata = metadata
 
     output_select = pe.Node(
         KeySelect(fields=["fmap", "fmap_ref", "fmap_coeff", "fmap_mask", "sdc_method"]),

From bf68f50ca619ba7df3f2b0e7f690c627d979560b Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sat, 23 Oct 2021 23:10:44 +0200
Subject: [PATCH 21/21] fix: incorrect joinfield on new node

---
 fmriprep/workflows/bold/base.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 846aa7ab5..e88eb57e4 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -1145,7 +1145,13 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             ]
         ),
         joinsource=("meepi_echos" if run_stc is True else "boldbuffer"),
-        joinfield=["bold_files"],
+        joinfield=[
+            "fieldmap",
+            "fieldwarp",
+            "corrected",
+            "corrected_ref",
+            "corrected_mask",
+        ],
         name="join_sdc_echos",
     )
 
@@ -1169,7 +1175,7 @@ def _dpop(list_of_lists):
             ("corrected", "inputnode.bold_file"),
         ]),
         (join_sdc_echos, bold_t2s_wf, [
-            ("corrected_mask", "inputnode.bold_mask"),
+            (("corrected_mask", pop_file), "inputnode.bold_mask"),
         ]),
         (join_sdc_echos, bold_t1_trans_wf, [
             # TEMPORARY: For the moment we can't use frame-wise fieldmaps