Merge pull request #188 from effigies/fix/nitransforms_convert

FIX: Convert LTA to ITK with nitransforms

smriprep/workflows/anatomical.py

@@ -18,10 +18,10 @@
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.freesurfer import (
     StructuralReference,
-    PatchedConcatenateLTA as ConcatenateLTA,
     PatchedLTAConvert as LTAConvert,
 )
 from niworkflows.interfaces.images import TemplateDimensions, Conform, ValidateImage
+from niworkflows.interfaces.nitransforms import ConcatenateXFMs
 from niworkflows.interfaces.utility import KeySelect
 from niworkflows.utils.misc import fix_multi_T1w_source_name, add_suffix
 from niworkflows.anat.ants import init_brain_extraction_wf, init_n4_only_wf
@@ -594,12 +594,10 @@ def init_anat_template_wf(longitudinal, omp_nthreads, num_t1w, name='anat_templa
     # 2. Reorient template to RAS, if needed (mri_robust_template may set to LIA)
     t1w_reorient = pe.Node(image.Reorient(), name='t1w_reorient')
 
-    concat_affines = pe.MapNode(
-        ConcatenateLTA(out_type='RAS2RAS', invert_out=True),
-        iterfield=['in_lta1', 'in_lta2'],
-        name='concat_affines')
-
-    lta_to_itk = pe.MapNode(LTAConvert(out_itk=True), iterfield=['in_lta'], name='lta_to_itk')
+    merge_xfm = pe.MapNode(niu.Merge(2), name='merge_xfm',
+                           iterfield=['in1', 'in2'], run_without_submitting=True)
+    concat_xfms = pe.MapNode(ConcatenateXFMs(inverse=True), name="concat_xfms",
+                             iterfield=['in_xfms'], run_without_submitting=True)
 
     def _set_threads(in_list, maximum):
         return min(len(in_list), maximum)
@@ -614,12 +612,12 @@ def _set_threads(in_list, maximum):
         (n4_correct, t1w_merge, [('output_image', 'in_files')]),
         (t1w_merge, t1w_reorient, [('out_file', 'in_file')]),
         # Combine orientation and template transforms
-        (t1w_conform_xfm, concat_affines, [('out_lta', 'in_lta1')]),
-        (t1w_merge, concat_affines, [('transform_outputs', 'in_lta2')]),
-        (concat_affines, lta_to_itk, [('out_file', 'in_lta')]),
+        (t1w_conform_xfm, merge_xfm, [('out_lta', 'in1')]),
+        (t1w_merge, merge_xfm, [('transform_outputs', 'in2')]),
+        (merge_xfm, concat_xfms, [('out', 'in_xfms')]),
         # Output
         (t1w_reorient, outputnode, [('out_file', 't1w_ref')]),
-        (lta_to_itk, outputnode, [('out_itk', 't1w_realign_xfm')]),
+        (concat_xfms, outputnode, [('out_xfm', 't1w_realign_xfm')]),
     ])
 
     return workflow

smriprep/workflows/outputs.py

@@ -5,7 +5,6 @@
 from nipype.interfaces import utility as niu
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.utils.misc import fix_multi_T1w_source_name
-from niworkflows.interfaces.freesurfer import PatchedLTAConvert as LTAConvert
 
 from ..interfaces import DerivativesDataSink
 
@@ -232,7 +231,7 @@ def init_anat_derivatives_wf(bids_root, freesurfer, num_t1w, output_dir,
         # It is necessary because from is a protected keyword (not allowed as argument name).
         ds_t1w_ref_xfms = pe.MapNode(
             DerivativesDataSink(base_directory=output_dir, to='T1w', mode='image', suffix='xfm',
-                                **{'from': 'orig'}),
+                                extension='txt', **{'from': 'orig'}),
             iterfield=['source_file', 'in_file'],
             name='ds_t1w_ref_xfms', run_without_submitting=True)
         workflow.connect([
@@ -243,17 +242,19 @@ def init_anat_derivatives_wf(bids_root, freesurfer, num_t1w, output_dir,
     if not freesurfer:
         return workflow
 
+    from niworkflows.interfaces.nitransforms import ConcatenateXFMs
     from niworkflows.interfaces.surf import Path2BIDS
 
     # FS native space transforms
-    lta2itk_fwd = pe.Node(LTAConvert(out_itk=True), name='lta2itk_fwd')
-    lta2itk_inv = pe.Node(LTAConvert(out_itk=True), name='lta2itk_inv')
+    lta2itk_fwd = pe.Node(ConcatenateXFMs(), name='lta2itk_fwd', run_without_submitting=True)
+    lta2itk_inv = pe.Node(ConcatenateXFMs(), name='lta2itk_inv', run_without_submitting=True)
     ds_t1w_fsnative = pe.Node(
         DerivativesDataSink(base_directory=output_dir, mode='image', to='fsnative', suffix='xfm',
-                            dismiss_entities=("session",), **{'from': 'T1w'}),
+                            extension="txt", dismiss_entities=("session",), **{'from': 'T1w'}),
         name='ds_t1w_fsnative', run_without_submitting=True)
     ds_fsnative_t1w = pe.Node(
         DerivativesDataSink(base_directory=output_dir, mode='image', to='T1w', suffix='xfm',
+                            extension="txt",
                             dismiss_entities=("session",), **{'from': 'fsnative'}),
         name='ds_fsnative_t1w', run_without_submitting=True)
     # Surfaces
@@ -274,12 +275,12 @@ def init_anat_derivatives_wf(bids_root, freesurfer, num_t1w, output_dir,
         name='ds_t1w_fsparc', run_without_submitting=True)
 
     workflow.connect([
-        (inputnode, lta2itk_fwd, [('t1w2fsnative_xfm', 'in_lta')]),
-        (inputnode, lta2itk_inv, [('fsnative2t1w_xfm', 'in_lta')]),
+        (inputnode, lta2itk_fwd, [('t1w2fsnative_xfm', 'in_xfms')]),
+        (inputnode, lta2itk_inv, [('fsnative2t1w_xfm', 'in_xfms')]),
         (t1w_name, ds_t1w_fsnative, [('out', 'source_file')]),
-        (lta2itk_fwd, ds_t1w_fsnative, [('out_itk', 'in_file')]),
+        (lta2itk_fwd, ds_t1w_fsnative, [('out_xfm', 'in_file')]),
         (t1w_name, ds_fsnative_t1w, [('out', 'source_file')]),
-        (lta2itk_inv, ds_fsnative_t1w, [('out_itk', 'in_file')]),
+        (lta2itk_inv, ds_fsnative_t1w, [('out_xfm', 'in_file')]),
         (inputnode, name_surfs, [('surfaces', 'in_file')]),
         (inputnode, ds_surfs, [('surfaces', 'in_file')]),
         (t1w_name, ds_surfs, [('out', 'source_file')]),