From 15e4d545f592dd6dc94d406c1ee6a51cee8d4073 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 09:35:43 -0400
Subject: [PATCH 01/19] Add "About" reportlet.

---
 qsirecon/interfaces/reports.py | 13 +-----
 qsirecon/workflows/base.py     | 74 +++++++++++++++++++++++++---------
 2 files changed, 57 insertions(+), 30 deletions(-)

diff --git a/qsirecon/interfaces/reports.py b/qsirecon/interfaces/reports.py
index 5b97842b..12c36b6f 100644
--- a/qsirecon/interfaces/reports.py
+++ b/qsirecon/interfaces/reports.py
@@ -39,23 +39,14 @@
 \t\t<li>Subject ID: {subject_id}</li>
 \t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
 \t\t<li>Diffusion-weighted series: inputs {n_dwis:d}, outputs {n_outputs:d}</li>
-{groupings}
-\t\t<li>Resampling targets: T1wACPC
+\t\t<li>FreeSurfer input: {freesurfer}</li>
+\t\t<li>Resampling targets: {output_spaces}</li>
 \t</ul>
 """
 
 DIFFUSION_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3>
 \t\t<ul class="elem-desc">
 \t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
-\t\t\t<li>Susceptibility distortion correction: {sdc}</li>
-\t\t\t<li>Coregistration Transform: {coregistration}</li>
-\t\t\t<li>Denoising Method: {denoise_method}</li>
-\t\t\t<li>Denoising Window: {denoise_window}</li>
-\t\t\t<li>HMC Transform: {hmc_transform}</li>
-\t\t\t<li>HMC Model: {hmc_model}</li>
-\t\t\t<li>DWI series resampled to spaces: T1wACPC</li>
-\t\t\t<li>Confounds collected: {confounds}</li>
-\t\t\t<li>Impute slice threshold: {impute_slice_threshold}</li>
 \t\t</ul>
 {validation_reports}
 """
diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 52728da0..41c5f928 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -6,6 +6,7 @@
 
 import json
 import os.path as op
+import sys
 from copy import deepcopy
 from glob import glob
 
@@ -16,6 +17,7 @@
 from nipype import __version__ as nipype_ver
 from nipype.utils.filemanip import split_filename
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+from niworkflows.utils.misc import fix_multi_T1w_source_name
 from packaging.version import Version
 from pkg_resources import resource_filename as pkgrf
 
@@ -76,6 +78,7 @@ def init_single_subject_recon_wf(subject_id):
     subject_id : str
         Single subject label
     """
+    from ..interfaces.bids import DerivativesDataSink
     from ..interfaces.ingress import QsiReconDWIIngress, UKBioBankDWIIngress
     from ..interfaces.interchange import (
         ReconWorkflowInputs,
@@ -84,6 +87,7 @@ def init_single_subject_recon_wf(subject_id):
         recon_workflow_anatomical_input_fields,
         recon_workflow_input_fields,
     )
+    from ..interfaces.reports import AboutSummary
     from .recon.anatomical import (
         init_dwi_recon_anatomical_workflow,
         init_highres_recon_anatomical_wf,
@@ -152,13 +156,14 @@ def init_single_subject_recon_wf(subject_id):
         # Get the preprocessed DWI and all the related preprocessed images
         if config.workflow.recon_input_pipeline == "qsiprep":
             dwi_ingress_nodes[dwi_file] = pe.Node(
-                QsiReconDWIIngress(dwi_file=dwi_file), name=wf_name + "_ingressed_dwi_data"
+                QsiReconDWIIngress(dwi_file=dwi_file),
+                name=f"{wf_name}_ingressed_dwi_data",
             )
 
         elif config.workflow.recon_input_pipeline == "ukb":
             dwi_ingress_nodes[dwi_file] = pe.Node(
                 UKBioBankDWIIngress(dwi_file=dwi_file, data_dir=str(dwi_input["path"].absolute())),
-                name=wf_name + "_ingressed_ukb_dwi_data",
+                name=f"{wf_name}_ingressed_ukb_dwi_data",
             )
             anat_ingress_nodes[dwi_file], available_anatomical_data = (
                 init_highres_recon_anatomical_wf(
@@ -167,7 +172,7 @@ def init_single_subject_recon_wf(subject_id):
                     extras_to_make=spec.get("anatomical", []),
                     pipeline_source="ukb",
                     needs_t1w_transform=needs_t1w_transform,
-                    name=wf_name + "_ingressed_ukb_anat_data",
+                    name=f"{wf_name}_ingressed_ukb_anat_data",
                 )
             )
 
@@ -179,7 +184,7 @@ def init_single_subject_recon_wf(subject_id):
                 prefer_dwi_mask=False,
                 needs_t1w_transform=needs_t1w_transform,
                 extras_to_make=spec.get("anatomical", []),
-                name=wf_name + "_dwi_specific_anat_wf",
+                name=f"{wf_name}_dwi_specific_anat_wf",
                 **available_anatomical_data,
             )
         )
@@ -187,42 +192,73 @@ def init_single_subject_recon_wf(subject_id):
         # This node holds all the inputs that will go to the recon workflow.
         # It is the definitive place to check what the input files are
         recon_full_inputs[dwi_file] = pe.Node(
-            ReconWorkflowInputs(), name=wf_name + "_recon_inputs"
+            ReconWorkflowInputs(),
+            name=f"{wf_name}_recon_inputs",
         )
 
         # This is the actual recon workflow for this dwi file
         dwi_recon_wfs[dwi_file] = init_dwi_recon_workflow(
             available_anatomical_data=dwi_available_anatomical_data,
             workflow_spec=spec,
-            name=wf_name + "_recon_wf",
+            name=f"{wf_name}_recon_wf",
         )
 
         # Connect the collected diffusion data (gradients, etc) to the inputnode
         workflow.connect([
             # The dwi data
             (dwi_ingress_nodes[dwi_file], recon_full_inputs[dwi_file], [
-                (trait, trait) for trait in qsiprep_output_names]),
+                (trait, trait) for trait in qsiprep_output_names
+            ]),
 
             # Session-specific anatomical data
-            (dwi_ingress_nodes[dwi_file], dwi_individual_anatomical_wfs[dwi_file],
-             [(trait, "inputnode." + trait) for trait in qsiprep_output_names]),
+            (dwi_ingress_nodes[dwi_file], dwi_individual_anatomical_wfs[dwi_file], [
+                (trait, f"inputnode.{trait}") for trait in qsiprep_output_names
+            ]),
 
             # subject dwi-specific anatomical to a special node in recon_full_inputs so
             # we have a record of what went in. Otherwise it would be lost in an IdentityInterface
-            (dwi_individual_anatomical_wfs[dwi_file], recon_full_inputs[dwi_file],
-             [("outputnode." + trait, trait) for trait in recon_workflow_anatomical_input_fields]),
+            (dwi_individual_anatomical_wfs[dwi_file], recon_full_inputs[dwi_file], [
+                (f"outputnode.{trait}", trait) for trait in recon_workflow_anatomical_input_fields
+            ]),
 
             # send the recon_full_inputs to the dwi recon workflow
-            (recon_full_inputs[dwi_file], dwi_recon_wfs[dwi_file],
-             [(trait, "inputnode." + trait) for trait in recon_workflow_input_fields]),
-
-            (anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep"
-             else anat_ingress_nodes[dwi_file],
-             dwi_individual_anatomical_wfs[dwi_file],
-             [(f"outputnode.{trait}", f"inputnode.{trait}")
-              for trait in anatomical_workflow_outputs])
+            (recon_full_inputs[dwi_file], dwi_recon_wfs[dwi_file], [
+                (trait, f"inputnode.{trait}") for trait in recon_workflow_input_fields
+            ]),
+
+            (
+                anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep"
+                else anat_ingress_nodes[dwi_file],
+                dwi_individual_anatomical_wfs[dwi_file],
+                [
+                    (f"outputnode.{trait}", f"inputnode.{trait}")
+                    for trait in anatomical_workflow_outputs
+                ]
+            ),
         ])  # fmt:skip
 
+    # Preprocessing of anatomical data (includes possible registration template)
+    about = pe.Node(
+        AboutSummary(version=config.environment.version, command=" ".join(sys.argv)),
+        name="about",
+        run_without_submitting=True,
+    )
+    ds_report_about = pe.Node(
+        DerivativesDataSink(
+            base_directory=config.execution.output_dir,
+            datatype="figures",
+            suffix="about",
+        ),
+        name="ds_report_about",
+        run_without_submitting=True,
+    )
+    workflow.connect([
+        (anat_ingress_nodes[dwi_file], ds_report_about, [
+            (('t1w_preproc', fix_multi_T1w_source_name), 'source_file'),
+        ]),
+        (about, ds_report_about, [('out_report', 'in_file')]),
+    ])  # fmt:skip
+
     # Fill-in datasinks of reportlets seen so far
     for node in workflow.list_node_names():
         if node.split(".")[-1].startswith("ds_report"):

From 724d98f34b5e76ecb38fc321349245fbbff593d2 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 09:51:12 -0400
Subject: [PATCH 02/19] Update base.py

---
 qsirecon/workflows/base.py | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 41c5f928..c71fdfdb 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -203,6 +203,12 @@ def init_single_subject_recon_wf(subject_id):
             name=f"{wf_name}_recon_wf",
         )
 
+        file_anat_ingress_node = (
+            anat_ingress_node
+            if config.workflow.recon_input_pipeline == "qsiprep"
+            else anat_ingress_nodes[dwi_file]
+        )
+
         # Connect the collected diffusion data (gradients, etc) to the inputnode
         workflow.connect([
             # The dwi data
@@ -226,15 +232,10 @@ def init_single_subject_recon_wf(subject_id):
                 (trait, f"inputnode.{trait}") for trait in recon_workflow_input_fields
             ]),
 
-            (
-                anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep"
-                else anat_ingress_nodes[dwi_file],
-                dwi_individual_anatomical_wfs[dwi_file],
-                [
-                    (f"outputnode.{trait}", f"inputnode.{trait}")
-                    for trait in anatomical_workflow_outputs
-                ]
-            ),
+            (file_anat_ingress_node, dwi_individual_anatomical_wfs[dwi_file], [
+                (f"outputnode.{trait}", f"inputnode.{trait}")
+                for trait in anatomical_workflow_outputs
+            ]),
         ])  # fmt:skip
 
     # Preprocessing of anatomical data (includes possible registration template)
@@ -253,7 +254,7 @@ def init_single_subject_recon_wf(subject_id):
         run_without_submitting=True,
     )
     workflow.connect([
-        (anat_ingress_nodes[dwi_file], ds_report_about, [
+        (file_anat_ingress_node, ds_report_about, [
             (('t1w_preproc', fix_multi_T1w_source_name), 'source_file'),
         ]),
         (about, ds_report_about, [('out_report', 'in_file')]),

From 92e7df4372244fcd12e6ffdc704f60df831ae4fe Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 10:10:19 -0400
Subject: [PATCH 03/19] Update base.py

---
 qsirecon/workflows/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index c71fdfdb..b3c2b4af 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -255,7 +255,7 @@ def init_single_subject_recon_wf(subject_id):
     )
     workflow.connect([
         (file_anat_ingress_node, ds_report_about, [
-            (('t1w_preproc', fix_multi_T1w_source_name), 'source_file'),
+            (('outputnode.t1w_preproc', fix_multi_T1w_source_name), 'source_file'),
         ]),
         (about, ds_report_about, [('out_report', 'in_file')]),
     ])  # fmt:skip

From ee3ec0b011804ba7e8878da2442c782411aecced Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 10:26:59 -0400
Subject: [PATCH 04/19] Try fixing again.

---
 qsirecon/interfaces/reports.py | 73 ++++++++++++++--------------------
 qsirecon/workflows/base.py     | 10 +++--
 2 files changed, 36 insertions(+), 47 deletions(-)

diff --git a/qsirecon/interfaces/reports.py b/qsirecon/interfaces/reports.py
index 12c36b6f..dfbc88c3 100644
--- a/qsirecon/interfaces/reports.py
+++ b/qsirecon/interfaces/reports.py
@@ -23,6 +23,7 @@
     CommandLineInputSpec,
     Directory,
     File,
+    InputMultiObject,
     InputMultiPath,
     SimpleInterface,
     Str,
@@ -35,12 +36,14 @@
 
 from .qc import createB0_ColorFA_Mask_Sprites, createSprite4D
 
-SUBJECT_TEMPLATE = """\t<ul class="elem-desc">
+SUBJECT_TEMPLATE = """\
+\t<ul class="elem-desc">
 \t\t<li>Subject ID: {subject_id}</li>
-\t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
-\t\t<li>Diffusion-weighted series: inputs {n_dwis:d}, outputs {n_outputs:d}</li>
-\t\t<li>FreeSurfer input: {freesurfer}</li>
-\t\t<li>Resampling targets: {output_spaces}</li>
+\t\t<li>Structural images: {n_t1w:d} T1-weighted {t2w}</li>
+\t\t<li>Diffusion-weighted series: {n_dwi:d}</li>
+\t\t<li>Standard output spaces: {std_spaces}</li>
+\t\t<li>Non-standard output spaces: {nstd_spaces}</li>
+\t\t<li>FreeSurfer reconstruction: {freesurfer_status}</li>
 \t</ul>
 """
 
@@ -121,9 +124,12 @@ class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
     t2w = InputMultiPath(File(exists=True), desc="T2w structural images")
     subjects_dir = Directory(desc="FreeSurfer subjects directory")
     subject_id = Str(desc="Subject ID")
-    dwi_groupings = traits.Dict(desc="groupings of DWI files and their output names")
-    output_spaces = traits.List(desc="Target spaces")
-    template = traits.Enum("MNI152NLin2009cAsym", desc="Template space")
+    dwi = InputMultiObject(
+        traits.Either(File(exists=True), traits.List(File(exists=True))),
+        desc="Preprocessed DWI series",
+    )
+    std_spaces = traits.List(Str, desc="list of standard spaces")
+    nstd_spaces = traits.List(Str, desc="list of non-standard spaces")
 
 
 class SubjectSummaryOutputSpec(SummaryOutputSpec):
@@ -139,49 +145,30 @@ class SubjectSummary(SummaryInterface):
     def _run_interface(self, runtime):
         if isdefined(self.inputs.subject_id):
             self._results["subject_id"] = self.inputs.subject_id
-        return super(SubjectSummary, self)._run_interface(runtime)
+        return super()._run_interface(runtime)
 
     def _generate_segment(self):
+        if not isdefined(self.inputs.subjects_dir):
+            freesurfer_status = "Not run"
+        else:
+            freesurfer_status = "Pre-existing directory"
+
         t2w_seg = ""
         if self.inputs.t2w:
-            t2w_seg = "(+ {:d} T2-weighted)".format(len(self.inputs.t2w))
-
-        # Add text for how the dwis are grouped
-        n_dwis = 0
-        n_outputs = 0
-        groupings = ""
-        if isdefined(self.inputs.dwi_groupings):
-            for output_fname, group_info in self.inputs.dwi_groupings.items():
-                n_outputs += 1
-                files_desc = []
-                files_desc.append(
-                    "\t\t\t<li>Scan group: %s (PE Dir %s)</li><ul>"
-                    % (output_fname, group_info["dwi_series_pedir"])
-                )
-                files_desc.append("\t\t\t\t<li>DWI Files: </li>")
-                for dwi_file in group_info["dwi_series"]:
-                    files_desc.append("\t\t\t\t\t<li> %s </li>" % dwi_file)
-                    n_dwis += 1
-                fieldmap_type = group_info["fieldmap_info"]["suffix"]
-                if fieldmap_type is not None:
-                    files_desc.append("\t\t\t\t<li>Fieldmap type: %s </li>" % fieldmap_type)
-
-                    for key, value in group_info["fieldmap_info"].items():
-                        files_desc.append("\t\t\t\t\t<li> %s: %s </li>" % (key, str(value)))
-                        n_dwis += 1
-                files_desc.append("</ul>")
-                groupings += GROUPING_TEMPLATE.format(
-                    output_name=output_fname, input_files="\n".join(files_desc)
-                )
+            t2w_seg = f"(+ {len(self.inputs.t2w):d} T2-weighted)"
+
+        # Add list of tasks with number of runs
+        dwi_series = self.inputs.dwi if isdefined(self.inputs.dwi) else []
+        dwi_series = [s[0] if isinstance(s, list) else s for s in dwi_series]
 
         return SUBJECT_TEMPLATE.format(
             subject_id=self.inputs.subject_id,
-            n_t1s=len(self.inputs.t1w),
+            n_t1w=len(self.inputs.t1w),
             t2w=t2w_seg,
-            n_dwis=n_dwis,
-            n_outputs=n_outputs,
-            groupings=groupings,
-            output_spaces="T1wACPC",
+            n_dwi=len(dwi_series),
+            std_spaces=", ".join(self.inputs.std_spaces),
+            nstd_spaces=", ".join(self.inputs.nstd_spaces),
+            freesurfer_status=freesurfer_status,
         )
 
 
diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index b3c2b4af..56402605 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -239,13 +239,18 @@ def init_single_subject_recon_wf(subject_id):
         ])  # fmt:skip
 
     # Preprocessing of anatomical data (includes possible registration template)
+    dwi_basename = fix_multi_T1w_source_name(dwi_recon_inputs)
     about = pe.Node(
-        AboutSummary(version=config.environment.version, command=" ".join(sys.argv)),
+        AboutSummary(
+            version=config.environment.version,
+            command=" ".join(sys.argv),
+        ),
         name="about",
         run_without_submitting=True,
     )
     ds_report_about = pe.Node(
         DerivativesDataSink(
+            source_file=dwi_basename,
             base_directory=config.execution.output_dir,
             datatype="figures",
             suffix="about",
@@ -254,9 +259,6 @@ def init_single_subject_recon_wf(subject_id):
         run_without_submitting=True,
     )
     workflow.connect([
-        (file_anat_ingress_node, ds_report_about, [
-            (('outputnode.t1w_preproc', fix_multi_T1w_source_name), 'source_file'),
-        ]),
         (about, ds_report_about, [('out_report', 'in_file')]),
     ])  # fmt:skip
 

From 5dba5e665e43e93c7962fa810797b57e249fb418 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 11:18:57 -0400
Subject: [PATCH 05/19] Add SubjectSummary.

---
 qsirecon/interfaces/utils.py | 19 ++++++++++++
 qsirecon/workflows/base.py   | 60 ++++++++++++++++++++++++++++--------
 2 files changed, 67 insertions(+), 12 deletions(-)

diff --git a/qsirecon/interfaces/utils.py b/qsirecon/interfaces/utils.py
index 308dd4a1..2fe37867 100644
--- a/qsirecon/interfaces/utils.py
+++ b/qsirecon/interfaces/utils.py
@@ -97,6 +97,25 @@ def _run_interface(self, runtime):
         return runtime
 
 
+class _GetUniqueInputSpec(BaseInterfaceInputSpec):
+    inlist = traits.List(mandatory=True, desc="list of things")
+
+
+class _GetUniqueOutputSpec(TraitedSpec):
+    outlist = traits.List()
+
+
+class GetUnique(SimpleInterface):
+    input_spec = _GetUniqueInputSpec
+    output_spec = _GetUniqueOutputSpec
+
+    def _run_interface(self, runtime):
+        in_list = self.inputs.inlist
+        in_list = [x for x in in_list if isdefined(x)]
+        self._results["outlist"] = sorted(list(set(in_list)))
+        return runtime
+
+
 def _resample_atlas(input_atlas, output_atlas, transform, ref_image):
     xform = ants.ApplyTransforms(
         transforms=[transform],
diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 56402605..485c7e93 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -15,6 +15,7 @@
 from dipy import __version__ as dipy_ver
 from nilearn import __version__ as nilearn_ver
 from nipype import __version__ as nipype_ver
+from nipype.interfaces import utility as niu
 from nipype.utils.filemanip import split_filename
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.utils.misc import fix_multi_T1w_source_name
@@ -87,7 +88,8 @@ def init_single_subject_recon_wf(subject_id):
         recon_workflow_anatomical_input_fields,
         recon_workflow_input_fields,
     )
-    from ..interfaces.reports import AboutSummary
+    from ..interfaces.reports import AboutSummary, SubjectSummary
+    from ..interfaces.utils import GetUnique
     from .recon.anatomical import (
         init_dwi_recon_anatomical_workflow,
         init_highres_recon_anatomical_wf,
@@ -142,6 +144,11 @@ def init_single_subject_recon_wf(subject_id):
             "Anatomical (T1w) available for recon: %s", available_anatomical_data
         )
 
+    aggregate_anatomical_nodes = pe.Node(
+        niu.Merge(len(dwi_recon_inputs)),
+        name="aggregate_anatomical_nodes",
+    )
+
     # create a processing pipeline for the dwis in each session
     dwi_recon_wfs = {}
     dwi_individual_anatomical_wfs = {}
@@ -149,7 +156,7 @@ def init_single_subject_recon_wf(subject_id):
     dwi_ingress_nodes = {}
     anat_ingress_nodes = {}
     print(dwi_recon_inputs)
-    for dwi_input in dwi_recon_inputs:
+    for i_run, dwi_input in enumerate(dwi_recon_inputs):
         dwi_file = dwi_input["bids_dwi_file"]
         wf_name = _get_wf_name(dwi_file)
 
@@ -159,6 +166,7 @@ def init_single_subject_recon_wf(subject_id):
                 QsiReconDWIIngress(dwi_file=dwi_file),
                 name=f"{wf_name}_ingressed_dwi_data",
             )
+            anat_ingress_nodes[dwi_file] = anat_ingress_node
 
         elif config.workflow.recon_input_pipeline == "ukb":
             dwi_ingress_nodes[dwi_file] = pe.Node(
@@ -176,6 +184,13 @@ def init_single_subject_recon_wf(subject_id):
                 )
             )
 
+        # Aggregate the anatomical data from all the dwi files
+        workflow.connect([
+            (anat_ingress_nodes[dwi_file], aggregate_anatomical_nodes, [
+                ("outputnode.t1_preproc", f"in{i_run + 1}")
+            ]),
+        ])  # fmt:skip
+
         # Create scan-specific anatomical data (mask, atlas configs, odf ROIs for reports)
         print(available_anatomical_data)
         dwi_individual_anatomical_wfs[dwi_file], dwi_available_anatomical_data = (
@@ -203,12 +218,6 @@ def init_single_subject_recon_wf(subject_id):
             name=f"{wf_name}_recon_wf",
         )
 
-        file_anat_ingress_node = (
-            anat_ingress_node
-            if config.workflow.recon_input_pipeline == "qsiprep"
-            else anat_ingress_nodes[dwi_file]
-        )
-
         # Connect the collected diffusion data (gradients, etc) to the inputnode
         workflow.connect([
             # The dwi data
@@ -232,7 +241,7 @@ def init_single_subject_recon_wf(subject_id):
                 (trait, f"inputnode.{trait}") for trait in recon_workflow_input_fields
             ]),
 
-            (file_anat_ingress_node, dwi_individual_anatomical_wfs[dwi_file], [
+            (anat_ingress_nodes[dwi_file], dwi_individual_anatomical_wfs[dwi_file], [
                 (f"outputnode.{trait}", f"inputnode.{trait}")
                 for trait in anatomical_workflow_outputs
             ]),
@@ -258,9 +267,36 @@ def init_single_subject_recon_wf(subject_id):
         name="ds_report_about",
         run_without_submitting=True,
     )
-    workflow.connect([
-        (about, ds_report_about, [('out_report', 'in_file')]),
-    ])  # fmt:skip
+    workflow.connect([(about, ds_report_about, [("out_report", "in_file")])])
+
+    reduce_t1_preproc = pe.Node(
+        GetUnique(),
+        name="reduce_t1_preproc",
+    )
+    workflow.connect([(aggregate_anatomical_nodes, reduce_t1_preproc, [("out", "inlist")])])
+    summary = pe.Node(
+        SubjectSummary(
+            subject_id=subject_id,
+            subjects_dir=config.execution.fs_subjects_dir,
+            std_spaces=["MNIInfant" if config.workflow.infant else "MNI152NLin2009cAsym"],
+            nstd_spaces=[],
+            dwi=dwi_recon_inputs,
+        ),
+        name="summary",
+        run_without_submitting=True,
+    )
+    workflow.connect([(reduce_t1_preproc, summary, [("out", "t1w")])])
+    ds_report_summary = pe.Node(
+        DerivativesDataSink(
+            source_file=dwi_basename,
+            base_directory=config.execution.output_dir,
+            datatype="figures",
+            suffix="summary",
+        ),
+        name="ds_report_summary",
+        run_without_submitting=True,
+    )
+    workflow.connect([(summary, ds_report_summary, [("out_report", "in_file")])])
 
     # Fill-in datasinks of reportlets seen so far
     for node in workflow.list_node_names():

From ee6ede03f99cfa3c39083fe6c00e3e5b9a0154e8 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 11:32:12 -0400
Subject: [PATCH 06/19] Update base.py

---
 qsirecon/workflows/base.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 485c7e93..7c800442 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -156,6 +156,7 @@ def init_single_subject_recon_wf(subject_id):
     dwi_ingress_nodes = {}
     anat_ingress_nodes = {}
     print(dwi_recon_inputs)
+    dwi_files = [dwi_input["bids_dwi_file"] for dwi_input in dwi_recon_inputs]
     for i_run, dwi_input in enumerate(dwi_recon_inputs):
         dwi_file = dwi_input["bids_dwi_file"]
         wf_name = _get_wf_name(dwi_file)
@@ -248,7 +249,7 @@ def init_single_subject_recon_wf(subject_id):
         ])  # fmt:skip
 
     # Preprocessing of anatomical data (includes possible registration template)
-    dwi_basename = fix_multi_T1w_source_name(dwi_recon_inputs)
+    dwi_basename = fix_multi_T1w_source_name(dwi_files)
     about = pe.Node(
         AboutSummary(
             version=config.environment.version,
@@ -280,7 +281,7 @@ def init_single_subject_recon_wf(subject_id):
             subjects_dir=config.execution.fs_subjects_dir,
             std_spaces=["MNIInfant" if config.workflow.infant else "MNI152NLin2009cAsym"],
             nstd_spaces=[],
-            dwi=dwi_recon_inputs,
+            dwi=dwi_files,
         ),
         name="summary",
         run_without_submitting=True,

From 3e3f35e8694da59aa68c2ca9be0a97c7439950b5 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 11:42:54 -0400
Subject: [PATCH 07/19] Update reports.py

---
 qsirecon/interfaces/reports.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/qsirecon/interfaces/reports.py b/qsirecon/interfaces/reports.py
index dfbc88c3..a8efe4d4 100644
--- a/qsirecon/interfaces/reports.py
+++ b/qsirecon/interfaces/reports.py
@@ -122,7 +122,11 @@ def _run_interface(self, runtime):
 class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
     t1w = InputMultiPath(File(exists=True), desc="T1w structural images")
     t2w = InputMultiPath(File(exists=True), desc="T2w structural images")
-    subjects_dir = Directory(desc="FreeSurfer subjects directory")
+    subjects_dir = traits.Either(
+        Directory,
+        None,
+        desc="FreeSurfer subjects directory",
+    )
     subject_id = Str(desc="Subject ID")
     dwi = InputMultiObject(
         traits.Either(File(exists=True), traits.List(File(exists=True))),

From b58f18056925f09feafa13dd3429e0e89eff24a9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 11:47:01 -0400
Subject: [PATCH 08/19] Set nireports version.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8682f17e..d9557018 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ dependencies = [
     "nibabel <= 5.2.0",
     "nilearn == 0.10.1",
     "nipype == 1.8.6",
-    "nireports",
+    "nireports ~= 23.2.2",
     "niworkflows >=1.9,<= 1.10",
     "numpy <= 1.26.3",
     "pandas < 2.0.0",

From 33d7a1886757653f3566110f2bdbaf0882a0a66b Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 12:02:01 -0400
Subject: [PATCH 09/19] Update base.py

---
 qsirecon/workflows/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 7c800442..fcdd1369 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -286,7 +286,7 @@ def init_single_subject_recon_wf(subject_id):
         name="summary",
         run_without_submitting=True,
     )
-    workflow.connect([(reduce_t1_preproc, summary, [("out", "t1w")])])
+    workflow.connect([(reduce_t1_preproc, summary, [("outlist", "t1w")])])
     ds_report_summary = pe.Node(
         DerivativesDataSink(
             source_file=dwi_basename,

From d9e8b9af006d2873cb026d39622d6b8aa69c6920 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 12:20:42 -0400
Subject: [PATCH 10/19] Update io_spec.json

---
 qsirecon/data/io_spec.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/qsirecon/data/io_spec.json b/qsirecon/data/io_spec.json
index b4063143..8328183b 100644
--- a/qsirecon/data/io_spec.json
+++ b/qsirecon/data/io_spec.json
@@ -52,6 +52,7 @@
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<mu>}.{extension<txt|json>|txt}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<exemplarbundles>}.{extension<zip|json>|zip}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<connectivity>}.{extension<mat|json>|mat}",
+        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<about|summary>}.{extension<html>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<peaks>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<odfs|matrices>}.{extension<html|svg|png|json>}"

From 9095ff2cdbbc87220c9f3a7a05475d47db0e33db Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 12:37:29 -0400
Subject: [PATCH 11/19] Whoops!

---
 qsirecon/data/io_spec.json | 1 -
 qsirecon/workflows/base.py | 6 ++++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/qsirecon/data/io_spec.json b/qsirecon/data/io_spec.json
index 8328183b..b4063143 100644
--- a/qsirecon/data/io_spec.json
+++ b/qsirecon/data/io_spec.json
@@ -52,7 +52,6 @@
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<mu>}.{extension<txt|json>|txt}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<exemplarbundles>}.{extension<zip|json>|zip}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<connectivity>}.{extension<mat|json>|mat}",
-        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<about|summary>}.{extension<html>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<peaks>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<odfs|matrices>}.{extension<html|svg|png|json>}"
diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index fcdd1369..a664f190 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -263,7 +263,8 @@ def init_single_subject_recon_wf(subject_id):
             source_file=dwi_basename,
             base_directory=config.execution.output_dir,
             datatype="figures",
-            suffix="about",
+            desc="about",
+            suffix="T1w",
         ),
         name="ds_report_about",
         run_without_submitting=True,
@@ -292,7 +293,8 @@ def init_single_subject_recon_wf(subject_id):
             source_file=dwi_basename,
             base_directory=config.execution.output_dir,
             datatype="figures",
-            suffix="summary",
+            desc="summary",
+            suffix="T1w",
         ),
         name="ds_report_summary",
         run_without_submitting=True,

From 775442cd1051a833648e96b8efca01d44b73a6fc Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 12:49:44 -0400
Subject: [PATCH 12/19] Update io_spec.json

---
 qsirecon/data/io_spec.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qsirecon/data/io_spec.json b/qsirecon/data/io_spec.json
index b4063143..789ac39f 100644
--- a/qsirecon/data/io_spec.json
+++ b/qsirecon/data/io_spec.json
@@ -52,7 +52,7 @@
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<mu>}.{extension<txt|json>|txt}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<exemplarbundles>}.{extension<zip|json>|zip}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<connectivity>}.{extension<mat|json>|mat}",
-        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi>}.{extension<html|svg|png|json>}",
+        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi|T1w|T2w>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<peaks>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<odfs|matrices>}.{extension<html|svg|png|json>}"
     ]

From 77d956497ce139d5472c9b7e30ab7692e749830c Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 14:26:06 -0400
Subject: [PATCH 13/19] Copy HTML figures.

---
 qsirecon/cli/run.py      |  9 ++++++++-
 qsirecon/cli/workflow.py | 20 ++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/qsirecon/cli/run.py b/qsirecon/cli/run.py
index c192f234..7ede341a 100644
--- a/qsirecon/cli/run.py
+++ b/qsirecon/cli/run.py
@@ -172,7 +172,7 @@ def main():
 
         from ..reports.core import generate_reports
         from ..workflows.base import _load_recon_spec
-        from .workflow import copy_boilerplate
+        from .workflow import copy_boilerplate, copy_reportlets
 
         # Generate reports phase
         session_list = config.execution.get().get("bids_filters", {}).get("dwi", {}).get("session")
@@ -201,6 +201,13 @@ def main():
             # Copy the boilerplate files
             copy_boilerplate(config.execution.output_dir, suffix_dir)
 
+            # Copy general reportlets
+            copy_reportlets(
+                config.execution.output_dir,
+                suffix_dir,
+                config.execution.participant_label,
+            )
+
             suffix_failed_reports = generate_reports(
                 config.execution.participant_label,
                 suffix_dir,
diff --git a/qsirecon/cli/workflow.py b/qsirecon/cli/workflow.py
index 5466a32e..457eeabe 100644
--- a/qsirecon/cli/workflow.py
+++ b/qsirecon/cli/workflow.py
@@ -239,3 +239,23 @@ def copy_boilerplate(in_dir, out_dir):
     for ext, citation_file in citation_files.items():
         if citation_file.exists():
             shutil.copy(citation_file, out_logs_path / f"CITATION.{ext}")
+
+
+def copy_reportlets(in_dir, out_dir, participant_label):
+    import shutil
+
+    in_path = Path(in_dir)
+    out_path = Path(out_dir)
+
+    subject_htmls = (in_path / participant_label).glob("figures/*.html")
+    for subject_html in subject_htmls:
+        out_html = out_path / subject_html.relative_to(in_path)
+        out_html.parent.mkdir(exist_ok=True, parents=True)
+        shutil.copy(subject_html, out_html)
+
+    # Session-wise reportlets
+    session_htmls = (in_path / participant_label).glob("ses-*/figures/*.html")
+    for session_html in session_htmls:
+        out_html = out_path / session_html.relative_to(in_path)
+        out_html.parent.mkdir(exist_ok=True, parents=True)
+        shutil.copy(session_html, out_html)

From d087179c3d57eeca29cd8afff85853662647f11f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 14:57:03 -0400
Subject: [PATCH 14/19] Fix!

---
 qsirecon/cli/workflow.py | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/qsirecon/cli/workflow.py b/qsirecon/cli/workflow.py
index 457eeabe..60b9246c 100644
--- a/qsirecon/cli/workflow.py
+++ b/qsirecon/cli/workflow.py
@@ -241,21 +241,22 @@ def copy_boilerplate(in_dir, out_dir):
             shutil.copy(citation_file, out_logs_path / f"CITATION.{ext}")
 
 
-def copy_reportlets(in_dir, out_dir, participant_label):
+def copy_reportlets(in_dir, out_dir, participant_labels):
     import shutil
 
     in_path = Path(in_dir)
     out_path = Path(out_dir)
 
-    subject_htmls = (in_path / participant_label).glob("figures/*.html")
-    for subject_html in subject_htmls:
-        out_html = out_path / subject_html.relative_to(in_path)
-        out_html.parent.mkdir(exist_ok=True, parents=True)
-        shutil.copy(subject_html, out_html)
-
-    # Session-wise reportlets
-    session_htmls = (in_path / participant_label).glob("ses-*/figures/*.html")
-    for session_html in session_htmls:
-        out_html = out_path / session_html.relative_to(in_path)
-        out_html.parent.mkdir(exist_ok=True, parents=True)
-        shutil.copy(session_html, out_html)
+    for subject_id in participant_labels:
+        subject_htmls = (in_path / subject_id).glob("figures/*.html")
+        for subject_html in subject_htmls:
+            out_html = out_path / subject_html.relative_to(in_path)
+            out_html.parent.mkdir(exist_ok=True, parents=True)
+            shutil.copy(subject_html, out_html)
+
+        # Session-wise reportlets
+        session_htmls = (in_path / subject_id).glob("ses-*/figures/*.html")
+        for session_html in session_htmls:
+            out_html = out_path / session_html.relative_to(in_path)
+            out_html.parent.mkdir(exist_ok=True, parents=True)
+            shutil.copy(session_html, out_html)

From ae671070b837c325b30bc2119923716c44f45dbd Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 15:18:49 -0400
Subject: [PATCH 15/19] FIX!!!

---
 qsirecon/cli/workflow.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/qsirecon/cli/workflow.py b/qsirecon/cli/workflow.py
index 60b9246c..937ac562 100644
--- a/qsirecon/cli/workflow.py
+++ b/qsirecon/cli/workflow.py
@@ -247,7 +247,16 @@ def copy_reportlets(in_dir, out_dir, participant_labels):
     in_path = Path(in_dir)
     out_path = Path(out_dir)
 
+    if not participant_labels:
+        from bids.layout import BIDSLayout
+
+        layout = BIDSLayout(out_dir, config="figures", validate=False)
+        participant_labels = layout.get_subjects()
+
     for subject_id in participant_labels:
+        if not subject_id.startswith("sub-"):
+            subject_id = f"sub-{subject_id}"
+
         subject_htmls = (in_path / subject_id).glob("figures/*.html")
         for subject_html in subject_htmls:
             out_html = out_path / subject_html.relative_to(in_path)

From a42ef41b8bb4133cad1c05b23513be6626d0a960 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 15:37:11 -0400
Subject: [PATCH 16/19] Remove unused elements.

---
 qsirecon/interfaces/reports.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/qsirecon/interfaces/reports.py b/qsirecon/interfaces/reports.py
index a8efe4d4..ee498e8c 100644
--- a/qsirecon/interfaces/reports.py
+++ b/qsirecon/interfaces/reports.py
@@ -47,27 +47,14 @@
 \t</ul>
 """
 
-DIFFUSION_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3>
-\t\t<ul class="elem-desc">
-\t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
-\t\t</ul>
-{validation_reports}
-"""
-
 ABOUT_TEMPLATE = """\t<ul>
 \t\t<li>QSIRecon version: {version}</li>
 \t\t<li>QSIRecon command: <code>{command}</code></li>
-\t\t<li>Date preprocessed: {date}</li>
+\t\t<li>Date postprocessed: {date}</li>
 \t</ul>
 </div>
 """
 
-GROUPING_TEMPLATE = """\t<ul>
-\t\t<li>Output Name: {output_name}</li>
-{input_files}
-</ul>
-"""
-
 INTERACTIVE_TEMPLATE = """
 <script src="https://unpkg.com/vue"></script>
 <script src="https://nipreps.github.io/dmriprep-viewer/dmriprepReport.umd.min.js"></script>

From 14849641f9100feeaebd8f21d4f793b6aafa5fef Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 16:07:00 -0400
Subject: [PATCH 17/19] Try using MapNodes.

---
 qsirecon/cli/run.py        | 19 ++-----------
 qsirecon/cli/workflow.py   | 30 ---------------------
 qsirecon/config.py         | 13 +++++++++
 qsirecon/workflows/base.py | 55 ++++++++++++++++++++++----------------
 4 files changed, 47 insertions(+), 70 deletions(-)

diff --git a/qsirecon/cli/run.py b/qsirecon/cli/run.py
index 7ede341a..892a747f 100644
--- a/qsirecon/cli/run.py
+++ b/qsirecon/cli/run.py
@@ -171,8 +171,7 @@ def main():
     finally:
 
         from ..reports.core import generate_reports
-        from ..workflows.base import _load_recon_spec
-        from .workflow import copy_boilerplate, copy_reportlets
+        from .workflow import copy_boilerplate
 
         # Generate reports phase
         session_list = config.execution.get().get("bids_filters", {}).get("dwi", {}).get("session")
@@ -184,15 +183,8 @@ def main():
         )
         write_bidsignore(config.execution.output_dir)
 
-        workflow_spec = _load_recon_spec()
         # Compile list of output folders
-        # TODO: Retain QSIRecon pipeline names in the config object
-        qsirecon_suffixes = []
-        for node_spec in workflow_spec["nodes"]:
-            qsirecon_suffix = node_spec.get("qsirecon_suffix", None)
-            qsirecon_suffixes += [qsirecon_suffix] if qsirecon_suffix else []
-
-        qsirecon_suffixes = sorted(list(set(qsirecon_suffixes)))
+        qsirecon_suffixes = config.workflow.qsirecon_suffixes
         config.loggers.cli.info(f"QSIRecon pipeline suffixes: {qsirecon_suffixes}")
         failed_reports = []
         for qsirecon_suffix in qsirecon_suffixes:
@@ -201,13 +193,6 @@ def main():
             # Copy the boilerplate files
             copy_boilerplate(config.execution.output_dir, suffix_dir)
 
-            # Copy general reportlets
-            copy_reportlets(
-                config.execution.output_dir,
-                suffix_dir,
-                config.execution.participant_label,
-            )
-
             suffix_failed_reports = generate_reports(
                 config.execution.participant_label,
                 suffix_dir,
diff --git a/qsirecon/cli/workflow.py b/qsirecon/cli/workflow.py
index 937ac562..5466a32e 100644
--- a/qsirecon/cli/workflow.py
+++ b/qsirecon/cli/workflow.py
@@ -239,33 +239,3 @@ def copy_boilerplate(in_dir, out_dir):
     for ext, citation_file in citation_files.items():
         if citation_file.exists():
             shutil.copy(citation_file, out_logs_path / f"CITATION.{ext}")
-
-
-def copy_reportlets(in_dir, out_dir, participant_labels):
-    import shutil
-
-    in_path = Path(in_dir)
-    out_path = Path(out_dir)
-
-    if not participant_labels:
-        from bids.layout import BIDSLayout
-
-        layout = BIDSLayout(out_dir, config="figures", validate=False)
-        participant_labels = layout.get_subjects()
-
-    for subject_id in participant_labels:
-        if not subject_id.startswith("sub-"):
-            subject_id = f"sub-{subject_id}"
-
-        subject_htmls = (in_path / subject_id).glob("figures/*.html")
-        for subject_html in subject_htmls:
-            out_html = out_path / subject_html.relative_to(in_path)
-            out_html.parent.mkdir(exist_ok=True, parents=True)
-            shutil.copy(subject_html, out_html)
-
-        # Session-wise reportlets
-        session_htmls = (in_path / subject_id).glob("ses-*/figures/*.html")
-        for session_html in session_htmls:
-            out_html = out_path / session_html.relative_to(in_path)
-            out_html.parent.mkdir(exist_ok=True, parents=True)
-            shutil.copy(session_html, out_html)
diff --git a/qsirecon/config.py b/qsirecon/config.py
index ca575c43..5b62471f 100644
--- a/qsirecon/config.py
+++ b/qsirecon/config.py
@@ -553,6 +553,19 @@ class workflow(_Config):
     """Recon workflow specification."""
     output_resolution = None
     """Isotropic voxel size for outputs."""
+    qsirecon_suffixes = []
+    """List of reconstruction workflow names, derived from the recon_spec."""
+
+    def init(cls):
+        from .workflows.base import _load_recon_spec
+
+        workflow_spec = _load_recon_spec(cls.recon_spec)
+        qsirecon_suffixes = []
+        for node_spec in workflow_spec["nodes"]:
+            qsirecon_suffix = node_spec.get("qsirecon_suffix", None)
+            qsirecon_suffixes += [qsirecon_suffix] if qsirecon_suffix else []
+
+        cls.qsirecon_suffixes = sorted(list(set(qsirecon_suffixes)))
 
 
 class loggers:
diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 592c6d22..5faf34bf 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -96,7 +96,7 @@ def init_single_subject_recon_wf(subject_id):
     )
     from .recon.build_workflow import init_dwi_recon_workflow
 
-    spec = _load_recon_spec()
+    spec = _load_recon_spec(config.workflow.recon_spec)
     dwi_recon_inputs = _get_iterable_dwi_inputs(subject_id)
 
     workflow = Workflow(name=f"sub-{subject_id}_{spec['name']}")
@@ -250,6 +250,13 @@ def init_single_subject_recon_wf(subject_id):
 
     # Preprocessing of anatomical data (includes possible registration template)
     dwi_basename = fix_multi_T1w_source_name(dwi_files)
+
+    reduce_t1_preproc = pe.Node(
+        GetUnique(),
+        name="reduce_t1_preproc",
+    )
+    workflow.connect([(aggregate_anatomical_nodes, reduce_t1_preproc, [("out", "inlist")])])
+
     about = pe.Node(
         AboutSummary(
             version=config.environment.version,
@@ -258,24 +265,6 @@ def init_single_subject_recon_wf(subject_id):
         name="about",
         run_without_submitting=True,
     )
-    ds_report_about = pe.Node(
-        DerivativesDataSink(
-            source_file=dwi_basename,
-            base_directory=config.execution.output_dir,
-            datatype="figures",
-            desc="about",
-            suffix="T1w",
-        ),
-        name="ds_report_about",
-        run_without_submitting=True,
-    )
-    workflow.connect([(about, ds_report_about, [("out_report", "in_file")])])
-
-    reduce_t1_preproc = pe.Node(
-        GetUnique(),
-        name="reduce_t1_preproc",
-    )
-    workflow.connect([(aggregate_anatomical_nodes, reduce_t1_preproc, [("out", "inlist")])])
     summary = pe.Node(
         SubjectSummary(
             subject_id=subject_id,
@@ -288,17 +277,38 @@ def init_single_subject_recon_wf(subject_id):
         run_without_submitting=True,
     )
     workflow.connect([(reduce_t1_preproc, summary, [("outlist", "t1w")])])
-    ds_report_summary = pe.Node(
+
+    suffix_dirs = []
+    for qsirecon_suffix in config.workflow.qsirecon_suffixes:
+        suffix_dir = str(config.execution.output_dir / f"qsirecon-{qsirecon_suffix}")
+        suffix_dirs.append(suffix_dir)
+
+    ds_report_about = pe.MapNode(
+        DerivativesDataSink(
+            source_file=dwi_basename,
+            datatype="figures",
+            desc="about",
+            suffix="T1w",
+        ),
+        name="ds_report_about",
+        run_without_submitting=True,
+        iterfield=["base_directory"],
+    )
+    ds_report_about.inputs.base_directory = suffix_dirs
+    workflow.connect([(about, ds_report_about, [("out_report", "in_file")])])
+
+    ds_report_summary = pe.MapNode(
         DerivativesDataSink(
             source_file=dwi_basename,
-            base_directory=config.execution.output_dir,
             datatype="figures",
             desc="summary",
             suffix="T1w",
         ),
         name="ds_report_summary",
         run_without_submitting=True,
+        iterfield=["base_directory"],
     )
+    ds_report_summary.inputs.base_directory = suffix_dirs
     workflow.connect([(summary, ds_report_summary, [("out_report", "in_file")])])
 
     # Fill-in datasinks of reportlets seen so far
@@ -321,10 +331,9 @@ def _get_wf_name(dwi_file):
     return "_".join(tokens[:-1]).replace("-", "_")
 
 
-def _load_recon_spec():
+def _load_recon_spec(spec_name):
     from ..utils.sloppy_recon import make_sloppy
 
-    spec_name = config.workflow.recon_spec
     prepackaged_dir = pkgrf("qsirecon", "data/pipelines")
     prepackaged = [op.split(fname)[1][:-5] for fname in glob(prepackaged_dir + "/*.json")]
     if op.exists(spec_name):

From 2c340492cc8cb58d12d0cfd49b476040ea20edee Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 16:17:24 -0400
Subject: [PATCH 18/19] Update config.py

---
 qsirecon/config.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/qsirecon/config.py b/qsirecon/config.py
index 5b62471f..1b491a18 100644
--- a/qsirecon/config.py
+++ b/qsirecon/config.py
@@ -556,6 +556,7 @@ class workflow(_Config):
     qsirecon_suffixes = []
     """List of reconstruction workflow names, derived from the recon_spec."""
 
+    @classmethod
     def init(cls):
         from .workflows.base import _load_recon_spec
 

From bcd8bcd2d7d576d7bd0c15e90c5f21c96eed090f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 19 Aug 2024 17:07:26 -0400
Subject: [PATCH 19/19] Update base.py

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

diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
index 5faf34bf..ab73cf48 100644
--- a/qsirecon/workflows/base.py
+++ b/qsirecon/workflows/base.py
@@ -66,6 +66,11 @@ def init_qsirecon_wf():
         log_dir.mkdir(exist_ok=True, parents=True)
         config.to_filename(log_dir / "qsirecon.toml")
 
+        # Dump a copy of the recon spec into the log directory as well
+        recon_spec = _load_recon_spec(config.workflow.recon_spec)
+        with open(log_dir / "recon_spec.json", "w") as f:
+            json.dump(recon_spec, f, indent=2, sort_keys=True)
+
     return qsirecon_wf
 
 
@@ -342,6 +347,7 @@ def _load_recon_spec(spec_name):
         recon_spec = op.join(prepackaged_dir + "/{}.json".format(spec_name))
     else:
         raise Exception("{} is not a file that exists or in {}".format(spec_name, prepackaged))
+
     with open(recon_spec, "r") as f:
         try:
             spec = json.load(f)
@@ -350,6 +356,7 @@ def _load_recon_spec(spec_name):
     if config.execution.sloppy:
         config.loggers.workflow.warning("Forcing reconstruction to use unrealistic parameters")
         spec = make_sloppy(spec)
+
     return spec