Directly use fMRIPrep confounds.

nipreps · May 7, 2024 · cd14ae0 · cd14ae0
1 parent 2821b0d
commit cd14ae0
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Showing 2 changed files with 12 additions and 10 deletions.
diff --git a/src/fmripost_aroma/interfaces/aroma.py b/src/fmripost_aroma/interfaces/aroma.py
@@ -18,7 +18,7 @@
 
 
 class _AROMAClassifierInputSpec(BaseInterfaceInputSpec):
-    motpars = File(exists=True, desc="motion parameters")
+    motpars = File(exists=True, desc="motion parameters or general confounds file")
     mixing = File(exists=True, desc="mixing matrix")
     component_maps = File(exists=True, desc="thresholded z-statistic component maps")
     TR = traits.Float(desc="repetition time in seconds")
@@ -38,7 +38,7 @@ class AROMAClassifier(SimpleInterface):
 
     def _run_interface(self, runtime):
         TR = self.inputs.TR
-        motion_params = utils.load_motpars(self.inputs.motpars, source="FSL")
+        motion_params = utils.load_motpars(self.inputs.motpars, source="fmriprep")
         mixing = np.loadtxt(self.inputs.mixing)  # T x C
         component_maps = nb.load(self.inputs.component_maps)  # X x Y x Z x C
         if mixing.shape[1] != component_maps.shape[3]:

diff --git a/src/fmripost_aroma/workflows/aroma.py b/src/fmripost_aroma/workflows/aroma.py
@@ -26,6 +26,7 @@
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.interfaces.confounds import NormalizeMotionParams
 
 from fmripost_aroma import config
 from fmripost_aroma.interfaces.bids import DerivativesDataSink
@@ -78,6 +79,7 @@ def init_ica_aroma_wf(
     Parameters
     ----------
     bold_file
+        BOLD series used as name source for derivatives
     metadata : :obj:`dict`
         BIDS metadata for BOLD file
     susan_fwhm : :obj:`float`
@@ -86,12 +88,15 @@ def init_ica_aroma_wf(
 
     Inputs
     ------
+    bold_std
+        BOLD series in template space
+    bold_mask_std
+        BOLD series mask in template space
+    confounds
+        fMRIPrep-formatted confounds file, which must include the following columns:
+        "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z".
     skip_vols
         number of non steady state volumes
-    bold_mask
-        BOLD series mask in template space
-    movpar_file
-        SPM-formatted motion parameters file
 
     Outputs
     -------
@@ -156,9 +161,6 @@ def init_ica_aroma_wf(
         name="outputnode",
     )
 
-    # TODO: Convert confounds to FSL motpars file.
-    ...
-
     rm_non_steady_state = pe.Node(
         niu.Function(function=_remove_volumes, output_names=["bold_cut"]),
         name="rm_nonsteady",
@@ -237,7 +239,7 @@ def init_ica_aroma_wf(
     # Run the ICA-AROMA classifier
     ica_aroma = pe.Node(AROMAClassifier(TR=metadata["RepetitionTime"]))
     workflow.connect([
-        (inputnode, ica_aroma, [("movpar_file", "motion_parameters")]),
+        (inputnode, ica_aroma, [("confounds", "motion_parameters")]),
         (select_melodic_files, ica_aroma, [
             ("mixing", "mixing"),
             ("component_maps", "component_maps"),