Limit BASIL --slicedt argument to ascending slice orders (#348)

* Set PLDs as output of ComputeCBF interface.

* Limit BASIL slicedt to ascending slice orders.

* Don't remove NIFTI files for test_002.

* Pin new PyBIDS version.

* Update cbf.py

* Update.

aslprep/interfaces/cbf.py

@@ -426,6 +426,11 @@ class _ComputeCBFOutputSpec(TraitedSpec):
         None,
         desc="Arterial transit time map, in seconds. Only generated for multi-delay data.",
     )
+    plds = traits.Either(
+        File(exists=True),
+        None,
+        desc="Post-labeling delays. Only defined if slice-timing correction is applied.",
+    )
 
 
 class ComputeCBF(SimpleInterface):
@@ -520,6 +525,7 @@ def _run_interface(self, runtime):
         m0data = np.mean(m0data, axis=0)
         scaled_m0data = m0_scale * m0data
 
+        self._results["plds"] = None
         if "SliceTiming" in metadata:
             # Offset PLD(s) by slice times
             # This step builds a voxel-wise array of post-labeling delay values,
@@ -575,6 +581,7 @@ def _run_interface(self, runtime):
                 newpath=runtime.cwd,
             )
             pld_img.to_filename(pld_file)
+            self._results["plds"] = pld_file
 
         elif is_multi_pld:
             # Broadcast PLDs to voxels by PLDs

aslprep/workflows/asl/cbf.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for calculating CBF."""
+import numpy as np
 import pandas as pd
 from nipype.interfaces import utility as niu
 from nipype.interfaces.fsl import Info, MultiImageMaths
@@ -241,6 +242,7 @@ def init_compute_cbf_wf(
                 "mean_cbf",
                 "cbf_ts",  # Only calculated for single-delay data
                 "att",  # Only calculated for multi-delay data
+                "plds",
                 # SCORE/SCRUB outputs
                 "cbf_ts_score",
                 "mean_cbf_score",
@@ -382,6 +384,7 @@ def _getfiledir(file):
             ("cbf_ts", "cbf_ts"),
             ("mean_cbf", "mean_cbf"),
             ("att", "att"),
+            ("plds", "plds"),
         ]),
     ])
     # fmt:on
@@ -465,10 +468,18 @@ def _getfiledir(file):
 
         basil_kwargs = {}
         if "SliceTiming" in metadata.keys():
-            # This won't work for non-ascending slice orders.
-            basil_kwargs["slice_spacing"] = abs(
-                metadata["SliceTiming"][1] - metadata["SliceTiming"][0]
-            )
+            slicetime_diffs = np.unique(np.diff(metadata["SliceTiming"]))
+            # Check if slice times are monotonic
+            monotonic_slicetimes = slicetime_diffs.size == 1
+            # Check if slice times are ascending
+            ascending_slicetimes = np.all(slicetime_diffs > 0)
+            # Only set slicedt for ascending slice orders.
+            if monotonic_slicetimes and ascending_slicetimes:
+                basil_kwargs["slice_spacing"] = slicetime_diffs[0]
+            else:
+                config.loggers.interface.warning(
+                    "Slice times are not ascending. They will be ignored in the BASIL call."
+                )
 
         basilcbf = pe.Node(
             BASILCBF(

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     "pandas >= 0.24.0",
     "patsy",
     "psutil >= 5.4",
-    "pybids >= 0.13.2",
+    "pybids ~= 0.16.4",
     "pyyaml",
     "scipy == 1.10.1",  # 1.11 introduces backwards incompatible change to scipy.stats.mode that doesn't work with bundled SDCFlows
     "sdcflows",