remove slice-timing correction

nipreps · Aug 18, 2022 · d68baf6 · d68baf6
1 parent a14998e
commit d68baf6
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Showing 4 changed files with 3 additions and 53 deletions.
diff --git a/mriqc/cli/parser.py b/mriqc/cli/parser.py
@@ -397,12 +397,6 @@ def _bids_filter(value):
         help="DEPRECATED Final volume in functional timeseries that should be "
         "considered for preprocessing.",
     )
-    g_func.add_argument(
-        "--correct-slice-timing",
-        action="store_true",
-        default=False,
-        help="Perform slice timing correction.",
-    )
 
     latest = check_latest()
     if latest is not None and currentv < latest:

diff --git a/mriqc/config.py b/mriqc/config.py
@@ -489,8 +489,6 @@ class workflow(_Config):
     """Level of analysis."""
     biggest_file_gb = 1
     """Size of largest file in GB."""
-    correct_slice_timing = False
-    """Perform slice timing correction."""
     deoblique = False
     """Deoblique the functional scans during head motion correction preprocessing."""
     despike = False

diff --git a/mriqc/data/config-example.toml b/mriqc/data/config-example.toml
@@ -34,7 +34,6 @@ write_graph = false
 [workflow]
 analysis_level = [ "participant",]
 biggest_file_gb = 0.03619009628891945
-correct_slice_timing = false
 deoblique = false
 despike = false
 fd_thres = 0.2

diff --git a/mriqc/workflows/functional.py b/mriqc/workflows/functional.py
@@ -676,7 +676,7 @@ def hmc(name="fMRI_HMC"):
 
     """
     from nipype.algorithms.confounds import FramewiseDisplacement
-    from nipype.interfaces.afni import Despike, Refit, TShift, Volreg
+    from nipype.interfaces.afni import Despike, Refit, Volreg
 
     mem_gb = config.workflow.biggest_file_gb
 
@@ -713,54 +713,13 @@ def hmc(name="fMRI_HMC"):
     ])
     # fmt: on
 
-    # Slice timing correction, despiking, and deoblique
-
-    st_corr = pe.Node(TShift(outputtype="NIFTI_GZ"), name="TimeShifts")
+    # despiking, and deoblique
 
     deoblique_node = pe.Node(Refit(deoblique=True), name="deoblique")
 
     despike_node = pe.Node(Despike(outputtype="NIFTI_GZ"), name="despike")
 
-    if all(
-        (
-            config.workflow.correct_slice_timing,
-            config.workflow.despike,
-            config.workflow.deoblique,
-        )
-    ):
-
-        # fmt: off
-        workflow.connect([
-            (inputnode, st_corr, [("in_file", "in_file")]),
-            (st_corr, despike_node, [("out_file", "in_file")]),
-            (despike_node, deoblique_node, [("out_file", "in_file")]),
-            (deoblique_node, hmc, [("out_file", "in_file")]),
-        ])
-        # fmt: on
-    elif config.workflow.correct_slice_timing and config.workflow.despike:
-        # fmt: off
-        workflow.connect([
-            (inputnode, st_corr, [("in_file", "in_file")]),
-            (st_corr, despike_node, [("out_file", "in_file")]),
-            (despike_node, hmc, [("out_file", "in_file")]),
-        ])
-        # fmt: on
-    elif config.workflow.correct_slice_timing and config.workflow.deoblique:
-        # fmt: off
-        workflow.connect([
-            (inputnode, st_corr, [("in_file", "in_file")]),
-            (st_corr, deoblique_node, [("out_file", "in_file")]),
-            (deoblique_node, hmc, [("out_file", "in_file")]),
-        ])
-        # fmt: on
-    elif config.workflow.correct_slice_timing:
-        # fmt: off
-        workflow.connect([
-            (inputnode, st_corr, [("in_file", "in_file")]),
-            (st_corr, hmc, [("out_file", "in_file")]),
-        ])
-        # fmt: on
-    elif config.workflow.despike and config.workflow.deoblique:
+    if config.workflow.despike and config.workflow.deoblique:
         # fmt: off
         workflow.connect([
             (inputnode, despike_node, [("in_file", "in_file")]),