ENH: Improved testing of LTA handling - ITK-to-LTA, mri_concatenate_lta

nitransforms/tests/data/regressions/from-fsnative_to-bold_mode-image.lta

@@ -0,0 +1,30 @@
+# This file was generated with bbregister, with fMRIPrep-20.0.5's settings
+type      = 0 # LINEAR_VOX_TO_VOX
+nxforms   = 1
+mean      = 0.0000 0.0000 0.0000
+sigma     = 10000.0000
+1 4 4
+3.124095916748047e+00 -2.993918396532536e-02 -8.824434876441956e-02 3.380017089843750e+01
+-7.292380183935165e-02 -1.901555061340332e+00 -3.172848463058472e+00 2.405808868408203e+02
+-1.820227503776550e-02 2.479679346084595e+00 -2.434180974960327e+00 7.082101440429688e+01
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+src volume info
+valid = 1  # volume info valid
+filename = /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz
+volume = 64 64 34
+voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = 1.000000000000000e+00 2.800000000000000e+01 -3.100000000000000e+01
+dst volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/derivatives/ds000005/freesurfer-6.0.1/sub-01/mri/orig.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -9.999999403953552e-01
+zras   = 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
+cras   = -9.999847412109375e-01 -5.000015258789062e+00 -1.000038146972656e+00
+subject sub-01
+fscale 0.100000

nitransforms/tests/data/regressions/from-fsnative_to-bold_mode-image.tfm

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: AffineTransform_double_3_3
+Parameters: 0.99971085786819458 0.0058247237466275692 0.023335624486207962 0.0095805395394563675 0.79349809885025024 -0.608498215675354 -0.022061100229620934 0.60854566097259521 0.79321271181106567 -5.5388064384460449 -45.559787750244141 -48.801029205322266
+FixedParameters: 0 0 0

nitransforms/tests/data/regressions/from-fsnative_to-bold_mode-image_type-ras2ras.lta

@@ -0,0 +1,31 @@
+# Created with lta_convert
+# lta_convert --inlta from-fsnative_to-bold_mode-image.lta --outlta from-fsnative_to-bold_mode-image_type-ras2ras.lta
+type      = 1 # LINEAR_RAS_TO_RAS
+nxforms   = 1
+mean      = 0.0000 0.0000 0.0000
+sigma     = 10000.0000
+1 4 4
+9.997106194496155e-01 9.580537676811218e-03 2.206108532845974e-02 -4.897087097167969e+00
+5.824727471917868e-03 7.934973239898682e-01 -6.085451841354370e-01 -6.588146209716797e+01
+-2.333561331033707e-02 6.084975600242615e-01 7.932120561599731e-01 1.111579895019531e+01
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+src volume info
+valid = 1  # volume info valid
+filename = /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz
+volume = 64 64 34
+voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = 1.000000000000000e+00 2.800000000000000e+01 -3.100000000000000e+01
+dst volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/derivatives/ds000005/freesurfer-6.0.1/sub-01/mri/orig.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -9.999999403953552e-01
+zras   = 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
+cras   = -9.999847412109375e-01 -5.000015258789062e+00 -1.000038146972656e+00
+subject sub-01
+fscale 0.100000

nitransforms/tests/data/regressions/bbregister.lta → nitransforms/tests/data/regressions/from-scanner_to-bold_mode-image.lta

@@ -1,12 +1,14 @@
+# This file was generated with bbregister, with fMRIPrep-20.0.5's settings
+# mri_concatenate_lta from-fsnative_to-bold_mode-image.lta from-scanner_to-fsnative_mode-image.lta from-scanner_to-bold_mode-image.lta
 type      = 0 # LINEAR_VOX_TO_VOX
 nxforms   = 1
 mean      = 0.0000 0.0000 0.0000
 sigma     = 1.0000
 1 4 4
--3.124080896377563e+00 2.981145866215229e-02 8.914728462696075e-02 1.741926879882812e+02 
--1.405486371368170e-02 1.859627604484558e+00 -1.825850725173950e+00 5.312585067749023e+01 
-5.505303665995598e-02 1.426339745521545e+00 2.379452466964722e+00 1.154438781738281e+01 
-0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999998807907104e-01 
+-3.124080896377563e+00 2.981145866215229e-02 8.914728462696075e-02 1.741926879882812e+02
+-1.405486371368170e-02 1.859627604484558e+00 -1.825850725173950e+00 5.312585067749023e+01
+5.505303665995598e-02 1.426339745521545e+00 2.379452466964722e+00 1.154438781738281e+01
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999998807907104e-01
 src volume info
 valid = 1  # volume info valid
 filename = /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz

nitransforms/tests/data/regressions/from-scanner_to-bold_mode-image.tfm

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: AffineTransform_double_3_3
+Parameters: 0.99970638751983643 0.0059967394918203354 0.023489311337471008 0.0095396693795919418 0.79344195127487183 -0.60857224464416504 -0.02228684164583683 0.60861742496490479 0.7931513786315918 -5.5388941764831543 -45.574077606201172 -48.804073333740234
+FixedParameters: 0 0 0

nitransforms/tests/data/regressions/from-scanner_to-bold_mode-image_type-ras2ras.lta

@@ -0,0 +1,31 @@
+# Created with lta_convert
+# lta_convert --inlta from-scanner_to-bold_mode-image.lta --outlta from-scanner_to-bold_mode-image_type-ras2ras.lta
+type      = 1 # LINEAR_RAS_TO_RAS
+nxforms   = 1
+mean      = 0.0000 0.0000 0.0000
+sigma     = 1.0000
+1 4 4
+9.997058510780334e-01 9.539666585624218e-03 2.228682115674019e-02 -4.884338378906250e+00
+5.996740423142910e-03 7.934408783912659e-01 -6.086167693138123e-01 -6.589652252197266e+01
+-2.348928898572922e-02 6.085714697837830e-01 7.931506037712097e-01 1.110400390625000e+01
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999998807907104e-01
+src volume info
+valid = 1  # volume info valid
+filename = /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz
+volume = 64 64 34
+voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = 1.000000000000000e+00 2.800000000000000e+01 -3.100000000000000e+01
+dst volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/ds000005/sub-01/anat/sub-01_T1w.nii.gz
+volume = 160 192 192
+voxelsize = 1.000000000000000e+00 1.333333015441895e+00 1.333333015441895e+00
+xras   = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = -1.000000000000000e+00 -5.000030517578125e+00 -1.000030517578125e+00
+subject sub-01
+fscale 0.100000

nitransforms/tests/data/regressions/from-scanner_to-fsnative_mode-image.lta

@@ -0,0 +1,30 @@
+# This file was generated with mri_robust_register, with fMRIPrep-20.0.5's settings
+# mri_robust_register --satit --iscale --lta from-scanner_to-fsnative_mode-image.lta --mov T1_fsnative.nii.gz --dst T1_scanner.nii.gz
+
+type      = 1 # LINEAR_RAS_TO_RAS
+nxforms   = 1
+mean      = 129.0000 157.0000 132.0000
+sigma     = 10000.0000
+1 4 4
+9.999999403953552e-01 -1.698292035143822e-04 1.542967074783519e-04 -1.678466796875000e-04
+1.698438863968477e-04 9.999999403953552e-01 -9.513227996649221e-05 -1.318359375000000e-02
+-1.542805403005332e-04 9.515848068986088e-05 9.999999403953552e-01 -6.271362304687500e-03
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999403953552e-01
+src volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/derivatives/ds000005/freesurfer-6.0.1/sub-01/mri/T1.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -9.999999403953552e-01
+zras   = 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
+cras   = -9.999847412109375e-01 -5.000015258789062e+00 -1.000038146972656e+00
+dst volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/ds000005/sub-01/anat/sub-01_T1w.nii.gz
+volume = 160 192 192
+voxelsize = 1.000000000000000e+00 1.333333015441895e+00 1.333333015441895e+00
+xras   = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = -1.000000000000000e+00 -5.000030517578125e+00 -1.000030517578125e+00

nitransforms/tests/data/regressions/from-scanner_to-fsnative_mode-image.tfm

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: AffineTransform_double_3_3
+Parameters: 1 0.00016984390094876289 0.00015428056940436363 -0.00016982921806629747 1 -9.5158495241776109e-05 -0.00015429672203026712 9.513228724244982e-05 1 -0.00016911829879973084 -0.01318416278809309 0.0062701348215341568
+FixedParameters: 0 0 0

nitransforms/tests/test_conversions.py

@@ -2,20 +2,57 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Conversions between formats."""
 import numpy as np
+import pytest
 from .. import linear as _l
+from ..io import LinearTransformArray as LTA
 
 
-def test_conversions0(data_path):
+@pytest.mark.parametrize('filename', [
+    "from-fsnative_to-bold_mode-image",
+    "from-fsnative_to-scanner_mode-image",
+    "from-scanner_to-bold_mode-image",
+    "from-scanner_to-fsnative_mode-image",
+])
+def test_lta2itk_conversions(data_path, filename):
     """Check conversions between formats."""
-    lta = _l.load(data_path / "regressions" / "robust_register.lta", fmt="lta")
-    itk = _l.load(data_path / "regressions" / "robust_register.tfm", fmt="itk")
-
+    lta = _l.load(data_path / "regressions" / ".".join((filename, "lta")),
+                  fmt="lta")
+    itk = _l.load(data_path / "regressions" / ".".join((filename, "tfm")),
+                  fmt="itk")
     assert np.allclose(lta.matrix, itk.matrix)
 
 
-def test_conversions1(data_path):
+@pytest.mark.parametrize('filename,moving,reference', [
+    ("from-fsnative_to-bold_mode-image", "T1w_fsnative.nii.gz", "bold.nii.gz"),
+    ("from-fsnative_to-scanner_mode-image", "T1w_fsnative.nii.gz", "T1w_scanner.nii.gz"),
+    ("from-scanner_to-bold_mode-image", "T1w_scanner.nii.gz", "bold.nii.gz"),
+    ("from-scanner_to-fsnative_mode-image", "T1w_scanner.nii.gz", "T1w_fsnative.nii.gz"),
+])
+def test_itk2lta_conversions(data_path, tmp_path, filename, moving, reference):
     """Check conversions between formats."""
-    lta = _l.load(data_path / "regressions" / "bbregister.lta", fmt="lta")
-    itk = _l.load(data_path / "regressions" / "bbregister.tfm", fmt="itk")
+    itk = _l.load(data_path / "regressions" / "".join((filename, ".tfm")),
+                  fmt="itk")
+    itk.reference = data_path / "regressions" / reference
+    itk.to_filename(tmp_path / "test.lta", fmt="fs",
+                    moving=data_path / "regressions" / moving)
 
-    assert np.allclose(lta.matrix, itk.matrix)
+    converted_lta = LTA.from_filename(tmp_path / "test.lta")
+    expected_fname = data_path / "regressions" / "".join((filename, "_type-ras2ras.lta"))
+    if not expected_fname.exists():
+        expected_fname = data_path / "regressions" / "".join((filename, ".lta"))
+
+    exp_lta = LTA.from_filename(expected_fname)
+    assert np.allclose(converted_lta['xforms'][0]['m_L'],
+                       exp_lta['xforms'][0]['m_L'])
+
+
+def test_concatenation(data_path):
+    """Check replacement to lta_concat."""
+    lta0 = _l.load(data_path / "regressions" / "from-scanner_to-fsnative_mode-image.lta",
+                   fmt="lta")
+    lta1 = _l.load(data_path / "regressions" / "from-fsnative_to-bold_mode-image.lta", fmt="lta")
+
+    lta_combined = _l.load(data_path / "regressions" / "from-scanner_to-bold_mode-image.lta",
+                           fmt="lta")
+
+    assert np.allclose(lta1.matrix.dot(lta0.matrix), lta_combined.matrix)

nitransforms/tests/test_io.py

@@ -342,6 +342,8 @@ def test_Displacements(sw_tool):
             afni.AFNIDisplacementsField.from_image(field)
 
 
-@pytest.mark.parametrize('file_type, test_file', [(LTA, 'robust_register.lta')])
+@pytest.mark.parametrize('file_type, test_file', [
+    (LTA, 'from-fsnative_to-scanner_mode-image.lta')
+])
 def test_regressions(file_type, test_file, data_path):
     file_type.from_filename(data_path / 'regressions' / test_file)