Use user-requested parameters in regression (#596)

PennLINC · Oct 20, 2022 · 9000864 · 9000864
1 parent 27d79a7
commit 9000864
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Showing 5 changed files with 53 additions and 23 deletions.
diff --git a/.circleci/tests/test_Reg.py b/.circleci/tests/test_Reg.py
@@ -10,16 +10,28 @@
 def test_Reg_Nifti(data_dir):
     """Test NIFTI regression."""
     #  Specify inputs
-    in_file = data_dir + "/fmriprep/sub-colornest001/ses-1/func/" \
+    in_file = (
+        data_dir + "/fmriprep/sub-colornest001/ses-1/func/"
         "sub-colornest001_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
-    confounds = data_dir + "/fmriprep/sub-colornest001/ses-1/func/" \
+    )
+    confounds = (
+        data_dir + "/fmriprep/sub-colornest001/ses-1/func/"
         "sub-colornest001_ses-1_task-rest_run-2_desc-confounds_timeseries.tsv"
+    )
     TR = 0.5
-    mask = data_dir + "/fmriprep/sub-colornest001/ses-1/func/" \
+    mask = (
+        data_dir + "/fmriprep/sub-colornest001/ses-1/func/"
         "sub-colornest001_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+    )
     # Run regression
-    test_nifti = Regress(mask=mask, in_file=in_file,
-                         original_file=in_file, confounds=confounds, TR=TR)
+    test_nifti = Regress(
+        mask=mask,
+        in_file=in_file,
+        original_file=in_file,
+        confounds=confounds,
+        TR=TR,
+        params="36P",
+    )
     results = test_nifti.run()
 
     # Read in_file and regression results in, but ignore the 'Unnamed:0' column if present
@@ -50,16 +62,28 @@ def test_Reg_Nifti(data_dir):
 def test_Reg_Cifti(data_dir):
     """Test CIFTI regression."""
     # Specify inputs
-    in_file = data_dir + "/fmriprep/sub-colornest001/ses-1/func/" \
+    in_file = (
+        data_dir + "/fmriprep/sub-colornest001/ses-1/func/"
         "sub-colornest001_ses-1_task-rest_run-1_space-fsLR_den-91k_bold.dtseries.nii"
-    confounds = data_dir + "/fmriprep/sub-colornest001/ses-1/func/" \
+    )
+    confounds = (
+        data_dir + "/fmriprep/sub-colornest001/ses-1/func/"
         "sub-colornest001_ses-1_task-rest_run-1_desc-confounds_timeseries.tsv"
+    )
     TR = 0.5
-    mask = data_dir + "/fmriprep/sub-colornest001/ses-1/func/" \
+    mask = (
+        data_dir + "/fmriprep/sub-colornest001/ses-1/func/"
         "sub-colornest001_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+    )
     # Run regression
-    test_cifti = Regress(mask=mask, in_file=in_file,
-                         original_file=in_file, confounds=confounds, TR=TR)
+    test_cifti = Regress(
+        mask=mask,
+        in_file=in_file,
+        original_file=in_file,
+        confounds=confounds,
+        TR=TR,
+        params="36P",
+    )
     results = test_cifti.run()
 
     # Read in_file and regression results in, but ignore the 'Unnamed:0' column if present

diff --git a/xcp_d/interfaces/regression.py b/xcp_d/interfaces/regression.py
@@ -29,6 +29,8 @@ class _RegressInputSpec(BaseInterfaceInputSpec):
         exists=True,
         mandatory=True,
         desc="The fMRIPrep confounds tsv after censoring")
+    # TODO: Use Enum maybe?
+    params = traits.Str(exists=True, mandatory=True, desc="Parameter set to use.")
     TR = traits.Float(exists=True, mandatory=True, desc="Repetition time")
     mask = File(exists=False, mandatory=False, desc="Brain mask for nifti files")
     original_file = traits.Str(exists=True, mandatory=False,
@@ -69,14 +71,20 @@ def _run_interface(self, runtime):
         # Get the confound matrix
         # Do we have custom confounds?
         if self.inputs.custom_confounds and exists(self.inputs.custom_confounds):
-            confound = load_confound_matrix(original_file=self.inputs.original_file,
-                                            datafile=self.inputs.in_file,
-                                            custom_confounds=self.inputs.custom_confounds,
-                                            confound_tsv=self.inputs.confounds)
+            confound = load_confound_matrix(
+                original_file=self.inputs.original_file,
+                datafile=self.inputs.in_file,
+                custom_confounds=self.inputs.custom_confounds,
+                confound_tsv=self.inputs.confounds,
+                params=self.inputs.params,
+            )
         else:  # No custom confounds
-            confound = load_confound_matrix(original_file=self.inputs.original_file,
-                                            datafile=self.inputs.in_file,
-                                            confound_tsv=self.inputs.confounds)
+            confound = load_confound_matrix(
+                original_file=self.inputs.original_file,
+                datafile=self.inputs.in_file,
+                confound_tsv=self.inputs.confounds,
+                params=self.inputs.params,
+            )
         # for testing, let's write out the confounds file:
         confounds_file_output_name = fname_presuffix(
             self.inputs.confounds,

diff --git a/xcp_d/utils/confounds.py b/xcp_d/utils/confounds.py
@@ -300,7 +300,7 @@ def square_confound(confound):
 
 @fill_doc
 def load_confound_matrix(
-    datafile, original_file, custom_confounds=None, confound_tsv=None, params="36P"
+    datafile, original_file, params, custom_confounds=None, confound_tsv=None
 ):
     """Load a subset of the confounds associated with a given file.
 
@@ -310,11 +310,11 @@ def load_confound_matrix(
         BOLD file whose confounds we want.
     original_file :
        File used to find confounds json.
+    %(params)s
     custom_confounds : str or None, optional
         Custom confounds TSV if there is one. Default is None.
     confound_tsv : str or None, optional
         The path to the confounds TSV file. Default is None.
-    %(params)s
 
     Returns
     -------

diff --git a/xcp_d/workflow/bold.py b/xcp_d/workflow/bold.py
@@ -353,8 +353,7 @@ def init_boldpostprocess_wf(
         n_procs=omp_nthreads)
 
     regression_wf = pe.Node(
-        Regress(TR=TR,
-                original_file=bold_file),
+        Regress(TR=TR, original_file=bold_file, params=params),
         name="regression_wf",
         mem_gb=mem_gbx['timeseries'],
         n_procs=omp_nthreads)

diff --git a/xcp_d/workflow/cifti.py b/xcp_d/workflow/cifti.py
@@ -329,8 +329,7 @@ def init_ciftipostprocess_wf(
         n_procs=omp_nthreads)
 
     regression_wf = pe.Node(
-        Regress(TR=TR,
-                original_file=bold_file),
+        Regress(TR=TR, original_file=bold_file, params=params),
         name="regression_wf",
         mem_gb=mem_gbx['timeseries'],
         n_procs=omp_nthreads)