ENH: Beef-up LTA tests with one equivalent to mri_concatenate_lta

This PR adds more LTA and corresponding ITK conversions. The ITK
conversions have been calculated with ``lta_convert``. The original
NIfTI files have also been added to this PR for the implementation of
future tests.

Files have been named with some sort of BIDS derived nomenclature. Some
provenance has been recorded as initial comments of the LTA files.

Author: oesteban

nitransforms/tests/data/regressions/T1w_fsnative.nii.gz

@@ -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/T1w_scanner.nii.gz

@@ -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/bbregister.tfm

@@ -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/bold.nii.gz

@@ -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-fsnative_to-bold_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-fsnative_to-bold_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/data/regressions/robust_register.lta renamed to nitransforms/tests/data/regressions/from-fsnative_to-scanner_mode-image.lta

@@ -2,20 +2,32 @@
 # 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
 
 
-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):
-    """Check conversions between formats."""
-    lta = _l.load(data_path / "regressions" / "bbregister.lta", fmt="lta")
-    itk = _l.load(data_path / "regressions" / "bbregister.tfm", fmt="itk")
+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")
 
-    assert np.allclose(lta.matrix, itk.matrix)
+    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/data/regressions/robust_register.tfm renamed to nitransforms/tests/data/regressions/from-fsnative_to-scanner_mode-image.tfm

@@ -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)