Fix many things.

aslprep/interfaces/__init__.py

@@ -3,16 +3,17 @@
 """Nipype interfaces for aslprep."""
 from aslprep.interfaces.bids import DerivativesDataSink
 from aslprep.interfaces.confounds import GatherConfounds
-from aslprep.interfaces.plotting import ASLSummary, CBFSummary, CBFtsSummary
-from aslprep.interfaces.reports import AboutSummary, FunctionalSummary, SubjectSummary
+from aslprep.interfaces.plotting import ASLCarpetPlot, CBFSummaryPlot, CBFtsSummary
+from aslprep.interfaces.reports import AboutSummary, CBFSummary, FunctionalSummary, SubjectSummary
 
 __all__ = [
     "SubjectSummary",
     "FunctionalSummary",
     "AboutSummary",
     "GatherConfounds",
-    "ASLSummary",
+    "ASLCarpetPlot",
     "CBFSummary",
+    "CBFSummaryPlot",
     "CBFtsSummary",
     "DerivativesDataSink",
 ]

aslprep/interfaces/plotting.py

@@ -16,7 +16,7 @@
 from aslprep.utils.plotting import CBFPlot, CBFtsPlot, fMRIPlot
 
 
-class _ASLSummaryInputSpec(BaseInterfaceInputSpec):
+class _ASLCarpetPlotInputSpec(BaseInterfaceInputSpec):
     in_nifti = File(exists=True, mandatory=True, desc="input BOLD (4D NIfTI file)")
     in_cifti = File(exists=True, desc="input BOLD (CIFTI dense timeseries)")
     in_segm = File(exists=True, desc="volumetric segmentation corresponding to in_nifti")
@@ -36,15 +36,17 @@ class _ASLSummaryInputSpec(BaseInterfaceInputSpec):
     drop_trs = traits.Int(0, usedefault=True, desc="dummy scans")
 
 
-class _ASLSummaryOutputSpec(TraitedSpec):
+class _ASLCarpetPlotOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="written file path")
 
 
-class ASLSummary(SimpleInterface):
-    """Copy the x-form matrices from `hdr_file` to `out_file`."""
+class ASLCarpetPlot(SimpleInterface):
+    """Create a combined carpet/line plot for ASL time series data.
 
-    input_spec = _ASLSummaryInputSpec
-    output_spec = _ASLSummaryOutputSpec
+    Copy the x-form matrices from `hdr_file` to `out_file`."""
+
+    input_spec = _ASLCarpetPlotInputSpec
+    output_spec = _ASLCarpetPlotOutputSpec
 
     def _run_interface(self, runtime):
         self._results["out_file"] = fname_presuffix(
@@ -125,25 +127,25 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class _CBFSummaryInputSpec(BaseInterfaceInputSpec):
+class _CBFSummaryPlotInputSpec(BaseInterfaceInputSpec):
     cbf = File(exists=True, mandatory=True, desc="")
     label = traits.Str(exists=True, mandatory=True, desc="label")
     vmax = traits.Int(exists=True, default_value=90, mandatory=True, desc="max value of asl")
     ref_vol = File(exists=True, mandatory=True, desc="")
 
 
-class _CBFSummaryOutputSpec(TraitedSpec):
+class _CBFSummaryPlotOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="written file path")
 
 
-class CBFSummary(SimpleInterface):
+class CBFSummaryPlot(SimpleInterface):
     """Prepare an CBF summary plot for the report.
 
     This plot restricts CBF values to -20 (if there are negative values) or 0 (if not) to 100.
     """
 
-    input_spec = _CBFSummaryInputSpec
-    output_spec = _CBFSummaryOutputSpec
+    input_spec = _CBFSummaryPlotInputSpec
+    output_spec = _CBFSummaryPlotOutputSpec
 
     def _run_interface(self, runtime):
         self._results["out_file"] = fname_presuffix(

aslprep/interfaces/reports.py

@@ -38,6 +38,12 @@
 \t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
 \t\t\t<li>Susceptibility distortion correction: {sdc}</li>
 \t\t\t<li>Registration: {registration}</li>
+
+\t\t</ul>
+"""
+
+QC_TEMPLATE = """\t\t<h3 class="elem-title">QC Summary</h3>
+\t\t<ul class="elem-desc">
 \t\t\t<li>Confounds collected: {confounds}</li>
 \t\t\t<li>Motion summary measures: {motionparam}</li>
 \t\t\t<li>Coregistration quality: {coregindex}</li>
@@ -206,6 +212,35 @@ def _generate_segment(self):
 
         pedir = get_world_pedir(self.inputs.orientation, self.inputs.pe_direction)
 
+        if self.inputs.pe_direction is None:
+            pedir = "MISSING - Assuming Anterior-Posterior"
+        else:
+            pedir = {"i": "Left-Right", "j": "Anterior-Posterior"}[self.inputs.pe_direction[0]]
+
+        # the number of dummy scans was specified by the user and
+        # it is not equal to the number detected by the algorithm
+
+        # the number of dummy scans was not specified by the user
+
+        return FUNCTIONAL_TEMPLATE.format(
+            pedir=pedir,
+            sdc=self.inputs.distortion_correction,
+            registration=reg,
+            tr=self.inputs.tr,
+        )
+
+
+class _CBFSummaryInputSpec(BaseInterfaceInputSpec):
+    confounds_file = File(exists=True, mandatory=False, desc="Confounds file")
+    qc_file = File(exists=True, desc="qc file")
+
+
+class CBFSummary(SummaryInterface):
+    """A summary of a functional run, with QC measures included."""
+
+    input_spec = _CBFSummaryInputSpec
+
+    def _generate_segment(self):
         qcfile = pd.read_csv(self.inputs.qc_file)
         motionparam = f"FD : {round(qcfile['FD'][0], 4)}, rmsd: {round(qcfile['rmsd'][0], 4)} "
         coregindex = (
@@ -239,10 +274,6 @@ def _generate_segment(self):
             f"basil: {round(qcfile['NEG_BASIL_PERC'][0], 2)}, "
             f"pvc: {round(qcfile['NEG_PVC_PERC'][0], 2)} "
         )
-        if self.inputs.pe_direction is None:
-            pedir = "MISSING - Assuming Anterior-Posterior"
-        else:
-            pedir = {"i": "Left-Right", "j": "Anterior-Posterior"}[self.inputs.pe_direction[0]]
 
         if isdefined(self.inputs.confounds_file):
             with open(self.inputs.confounds_file) as cfh:
@@ -254,12 +285,8 @@ def _generate_segment(self):
 
         # the number of dummy scans was not specified by the user
 
-        return FUNCTIONAL_TEMPLATE.format(
-            pedir=pedir,
-            sdc=self.inputs.distortion_correction,
-            registration=reg,
+        return QC_TEMPLATE.format(
             confounds=re.sub(r"[\t ]+", ", ", conflist),
-            tr=self.inputs.tr,
             motionparam=motionparam,
             qei=qei,
             coregindex=coregindex,

aslprep/workflows/asl/base.py

@@ -722,9 +722,13 @@ def init_asl_preproc_wf(
             ("t1w_dseg", "inputnode.t1w_dseg"),
             ("mni2009c2anat_xfm", "inputnode.std2anat_xfm"),
         ]),
+        (asl_confounds_wf, plot_cbf_wf, [
+            ("outputnode.confounds_file", "inputnode.confounds_file"),
+        ]),
         (cbf_wf, plot_cbf_wf, [
             ("outputnode.score_outlier_index", "inputnode.score_outlier_index"),
         ]),
+        (cbf_qc_wf, plot_cbf_wf, [("outputnode.qc_file", "inputnode.qc_file")]),
         (asl_fit_wf, plot_cbf_wf, [
             ("outputnode.coreg_aslref", "inputnode.aslref"),
             ("outputnode.aslref2anat_xfm", "inputnode.aslref2anat_xfm"),

aslprep/workflows/asl/confounds.py

@@ -10,7 +10,7 @@
 from templateflow.api import get as get_template
 
 from aslprep.config import DEFAULT_MEMORY_MIN_GB
-from aslprep.interfaces import ASLSummary, DerivativesDataSink, GatherConfounds
+from aslprep.interfaces import ASLCarpetPlot, DerivativesDataSink, GatherConfounds
 from aslprep.interfaces.ants import ApplyTransforms
 
 
@@ -375,7 +375,7 @@ def init_carpetplot_wf(
 
     # Carpetplot and confounds plot
     conf_plot = pe.Node(
-        ASLSummary(
+        ASLCarpetPlot(
             tr=metadata["RepetitionTime"],
             confounds_list=confounds_list,
         ),

aslprep/workflows/asl/fit.py

@@ -372,7 +372,7 @@ def init_asl_fit_wf(
     )
 
     reduce_asl_file = pe.Node(
-        ReduceASLFiles(),
+        ReduceASLFiles(metadata=metadata),
         name="reduce_asl_file",
     )
     # fmt:off
@@ -401,7 +401,10 @@ def init_asl_fit_wf(
     # fmt:off
     workflow.connect([
         (hmcref_buffer, asl_hmc_wf, [("aslref", "inputnode.raw_ref_image")]),
-        (reduce_asl_file, asl_hmc_wf, [("asl_file", "inputnode.asl_file")]),
+        (reduce_asl_file, asl_hmc_wf, [
+            ("asl_file", "inputnode.asl_file"),
+            ("aslcontext", "inputnode.aslcontext"),
+        ]),
         (asl_hmc_wf, ds_hmc_wf, [("outputnode.xforms", "inputnode.xforms")]),
         (asl_hmc_wf, hmc_buffer, [
             ("outputnode.xforms", "hmc_xforms"),

aslprep/workflows/asl/plotting.py

@@ -9,7 +9,8 @@
 from aslprep.interfaces import DerivativesDataSink
 from aslprep.interfaces.ants import ApplyTransforms
 from aslprep.interfaces.confounds import GatherCBFConfounds
-from aslprep.interfaces.plotting import CBFByTissueTypePlot, CBFSummary
+from aslprep.interfaces.plotting import CBFByTissueTypePlot, CBFSummaryPlot
+from aslprep.interfaces.reports import CBFSummary
 from aslprep.utils.misc import _select_last_in_list
 from aslprep.workflows.asl.confounds import init_carpetplot_wf
 
@@ -49,6 +50,8 @@ def init_plot_cbf_wf(
                 "t1w_dseg",
                 "aslref2anat_xfm",
                 "std2anat_xfm",
+                "confounds_file",
+                "qc_file",
                 # If plot_timeseries is True
                 "crown_mask",
                 "acompcor_masks",
@@ -68,11 +71,24 @@ def init_plot_cbf_wf(
                 "mean_cbf_gm_basil",
                 "mean_cbf_wm_basil",  # unused
                 "att_basil",  # unused
-            ]
+            ],
         ),
         name="inputnode",
     )
 
+    summary = pe.Node(
+        CBFSummary(),
+        name="summary",
+        mem_gb=config.DEFAULT_MEMORY_MIN_GB,
+        run_without_submitting=True,
+    )
+    workflow.connect([
+        (inputnode, summary, [
+            ("confounds_file", "confounds_file"),
+            ("qc_file", "qc_file"),
+        ])
+    ])  # fmt:skip
+
     # Warp dseg file from T1w space to ASL reference space
     warp_t1w_dseg_to_aslref = pe.Node(
         ApplyTransforms(
@@ -168,7 +184,7 @@ def init_plot_cbf_wf(
         ])
         # fmt:on
 
-    cbf_summary = pe.Node(CBFSummary(label="cbf", vmax=100), name="cbf_summary", mem_gb=1)
+    cbf_summary = pe.Node(CBFSummaryPlot(label="cbf", vmax=100), name="cbf_summary", mem_gb=1)
 
     # fmt:off
     workflow.connect([
@@ -211,7 +227,7 @@ def init_plot_cbf_wf(
 
     if scorescrub:
         score_summary = pe.Node(
-            CBFSummary(label="score", vmax=100),
+            CBFSummaryPlot(label="score", vmax=100),
             name="score_summary",
             mem_gb=1,
         )
@@ -260,7 +276,7 @@ def init_plot_cbf_wf(
         # fmt:on
 
         scrub_summary = pe.Node(
-            CBFSummary(label="scrub", vmax=100),
+            CBFSummaryPlot(label="scrub", vmax=100),
             name="scrub_summary",
             mem_gb=1,
         )
@@ -310,7 +326,7 @@ def init_plot_cbf_wf(
 
     if basil:
         basil_summary = pe.Node(
-            CBFSummary(label="basil", vmax=100),
+            CBFSummaryPlot(label="basil", vmax=100),
             name="basil_summary",
             mem_gb=1,
         )
@@ -359,7 +375,7 @@ def init_plot_cbf_wf(
         # fmt:on
 
         pvc_summary = pe.Node(
-            CBFSummary(label="pvc", vmax=120),
+            CBFSummaryPlot(label="pvc", vmax=120),
             name="pvc_summary",
             mem_gb=1,
         )