Merge branch 'master' into fix_afni_allineate

Author: rmarkello

doc/images/nipype_architecture_overview2.png

@@ -7,6 +7,8 @@ def test_ACompCor_inputs():
     input_map = dict(components_file=dict(usedefault=True,
     ),
     header_prefix=dict(),
+    high_pass_cutoff=dict(usedefault=True,
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
@@ -19,11 +21,16 @@ def test_ACompCor_inputs():
     ),
     num_components=dict(usedefault=True,
     ),
+    pre_filter=dict(usedefault=True,
+    ),
     realigned_file=dict(mandatory=True,
     ),
     regress_poly_degree=dict(usedefault=True,
     ),
-    use_regress_poly=dict(usedefault=True,
+    repetition_time=dict(),
+    save_pre_filter=dict(),
+    use_regress_poly=dict(deprecated='0.15.0',
+    new_name='pre_filter',
     ),
     )
     inputs = ACompCor.input_spec()
@@ -35,6 +42,7 @@ def test_ACompCor_inputs():
 
 def test_ACompCor_outputs():
     output_map = dict(components_file=dict(),
+    pre_filter_file=dict(),
     )
     outputs = ACompCor.output_spec()
 

doc/images/nipype_architecture_overview2.svg

@@ -7,6 +7,8 @@ def test_TCompCor_inputs():
     input_map = dict(components_file=dict(usedefault=True,
     ),
     header_prefix=dict(),
+    high_pass_cutoff=dict(usedefault=True,
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
@@ -21,11 +23,16 @@ def test_TCompCor_inputs():
     ),
     percentile_threshold=dict(usedefault=True,
     ),
+    pre_filter=dict(usedefault=True,
+    ),
     realigned_file=dict(mandatory=True,
     ),
     regress_poly_degree=dict(usedefault=True,
     ),
-    use_regress_poly=dict(usedefault=True,
+    repetition_time=dict(),
+    save_pre_filter=dict(),
+    use_regress_poly=dict(deprecated='0.15.0',
+    new_name='pre_filter',
     ),
     )
     inputs = TCompCor.input_spec()
@@ -38,6 +45,7 @@ def test_TCompCor_inputs():
 def test_TCompCor_outputs():
     output_map = dict(components_file=dict(),
     high_variance_masks=dict(),
+    pre_filter_file=dict(),
     )
     outputs = TCompCor.output_spec()
 

nipype/algorithms/confounds.py

@@ -80,7 +80,7 @@ def test_compcor_no_regress_poly(self):
         self.run_cc(CompCor(realigned_file=self.realigned_file,
                             mask_files=self.mask_files,
                             mask_index=0,
-                            use_regress_poly=False),
+                            pre_filter=False),
                     [['0.4451946442', '-0.7683311482'],
                      ['-0.4285129505', '-0.0926034137'],
                      ['0.5721540256', '0.5608764842'],

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -15,10 +15,10 @@
                          Maskave, Means, OutlierCount,
                          QualityIndex, ROIStats, Retroicor,
                          Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
-                         TShift, Volreg, Warp, QwarpPlusMinus)
+                         TShift, Volreg, Warp, QwarpPlusMinus, Qwarp)
 from .svm import (SVMTest, SVMTrain)
-from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy, Edge3,
-                    Eval, FWHMx,
-                    MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
-                    Unifize, ZCutUp, GCOR,)
+from .utils import (AFNItoNIFTI, Autobox, Axialize, BrickStat, Calc, Cat, Copy,
+                    Edge3, Eval, FWHMx, MaskTool, Merge, Notes, NwarpApply,
+                    Refit, Resample, TCat, TStat, To3D, Unifize, ZCutUp, GCOR,
+                    Zcat, Zeropad)
 from .model import (Deconvolve, Remlfit)