From b755445a5bb250a0b83007a92d343c397480737a Mon Sep 17 00:00:00 2001 From: Michael Joseph Date: Thu, 6 Jun 2019 10:25:45 -0400 Subject: [PATCH 1/4] eddy_quad doesn't like = signs --- nipype/interfaces/fsl/epi.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index bbe84149c8..8c35a5b447 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -1246,7 +1246,7 @@ class EddyQuadInputSpec(FSLCommandInputSpec): idx_file = File( exists=True, mandatory=True, - argstr="--eddyIdx=%s", + argstr="--eddyIdx %s", desc=("File containing indices for all volumes into acquisition " "parameters") ) @@ -1259,35 +1259,35 @@ class EddyQuadInputSpec(FSLCommandInputSpec): mask_file = File( exists=True, mandatory=True, - argstr="--mask=%s", + argstr="--mask %s", desc="Binary mask file" ) bval_file = File( exists=True, mandatory=True, - argstr="--bvals=%s", + argstr="--bvals %s", desc="b-values file" ) bvec_file = File( exists=True, - argstr="--bvecs=%s", + argstr="--bvecs %s", desc=("b-vectors file - only used when .eddy_residuals " "file is present") ) output_dir = traits.Str( name_template='%s.qc', name_source=['base_name'], - argstr='--output-dir=%s', + argstr='--output-dir %s', desc="Output directory - default = '.qc'", ) field = File( exists=True, - argstr='--field=%s', + argstr='--field %s', desc="TOPUP estimated field (in Hz)", ) slice_spec = File( exists=True, - argstr='--slspec=%s', + argstr='--slspec %s', desc="Text file specifying slice/group acquisition", ) verbose = traits.Bool( @@ -1365,9 +1365,9 @@ class EddyQuad(FSLCommand): >>> quad.inputs.field = 'fieldmap_phase_fslprepared.nii' >>> quad.inputs.verbose = True >>> quad.cmdline - 'eddy_quad eddy_corrected --bvals=bvals.scheme --bvecs=bvecs.scheme \ ---field=fieldmap_phase_fslprepared.nii --eddyIdx=epi_index.txt \ ---mask=epi_mask.nii --output-dir=eddy_corrected.qc --eddyParams=epi_acqp.txt \ + 'eddy_quad eddy_corrected --bvals bvals.scheme --bvecs bvecs.scheme \ +--field fieldmap_phase_fslprepared.nii --eddyIdx epi_index.txt \ +--mask epi_mask.nii --output-dir eddy_corrected.qc --eddyParams epi_acqp.txt \ --verbose' >>> res = quad.run() # doctest: +SKIP From 1fc0507b448337e528447d59cf51ccc307bba7f6 Mon Sep 17 00:00:00 2001 From: Michael Joseph Date: Thu, 6 Jun 2019 12:12:59 -0400 Subject: [PATCH 2/4] ran make specs --- nipype/algorithms/tests/test_auto_ACompCor.py | 4 ++-- nipype/algorithms/tests/test_auto_TCompCor.py | 4 ++-- nipype/interfaces/fsl/tests/test_auto_EddyQuad.py | 14 +++++++------- .../interfaces/spm/tests/test_auto_Level1Design.py | 1 + 4 files changed, 12 insertions(+), 11 deletions(-) diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index 95a9f51a88..e28c77d467 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -25,8 +25,8 @@ def test_ACompCor_inputs(): realigned_file=dict(mandatory=True, ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), - save_metadata=dict(), - save_pre_filter=dict(), + save_metadata=dict(usedefault=True, ), + save_pre_filter=dict(usedefault=True, ), use_regress_poly=dict( deprecated='0.15.0', new_name='pre_filter', diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index 1e94ef4241..c3bdcac192 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -26,8 +26,8 @@ def test_TCompCor_inputs(): realigned_file=dict(mandatory=True, ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), - save_metadata=dict(), - save_pre_filter=dict(), + save_metadata=dict(usedefault=True, ), + save_pre_filter=dict(usedefault=True, ), use_regress_poly=dict( deprecated='0.15.0', new_name='pre_filter', diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py index 4302cdc312..a0d5085fbb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py @@ -12,25 +12,25 @@ def test_EddyQuad_inputs(): usedefault=True, ), bval_file=dict( - argstr='--bvals=%s', + argstr='--bvals %s', mandatory=True, ), - bvec_file=dict(argstr='--bvecs=%s', ), + bvec_file=dict(argstr='--bvecs %s', ), environ=dict( nohash=True, usedefault=True, ), - field=dict(argstr='--field=%s', ), + field=dict(argstr='--field %s', ), idx_file=dict( - argstr='--eddyIdx=%s', + argstr='--eddyIdx %s', mandatory=True, ), mask_file=dict( - argstr='--mask=%s', + argstr='--mask %s', mandatory=True, ), output_dir=dict( - argstr='--output-dir=%s', + argstr='--output-dir %s', name_source=['base_name'], name_template='%s.qc', ), @@ -39,7 +39,7 @@ def test_EddyQuad_inputs(): argstr='--eddyParams=%s', mandatory=True, ), - slice_spec=dict(argstr='--slspec=%s', ), + slice_spec=dict(argstr='--slspec %s', ), verbose=dict(argstr='--verbose', ), ) inputs = EddyQuad.input_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 7ad8ab8195..7dce3dda2a 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -10,6 +10,7 @@ def test_Level1Design_inputs(): mandatory=True, ), factor_info=dict(field='fact', ), + flags=dict(), global_intensity_normalization=dict(field='global', ), interscan_interval=dict( field='timing.RT', From bdf2d2f3858f4b8d02f66f58422fac82026513d8 Mon Sep 17 00:00:00 2001 From: Michael Joseph Date: Thu, 6 Jun 2019 20:03:33 -0400 Subject: [PATCH 3/4] forgot = --- nipype/interfaces/fsl/epi.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 8c35a5b447..f94bda1147 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -1253,7 +1253,7 @@ class EddyQuadInputSpec(FSLCommandInputSpec): param_file = File( exists=True, mandatory=True, - argstr="--eddyParams=%s", + argstr="--eddyParams %s", desc="File containing acquisition parameters" ) mask_file = File( From b98990035705bde9fff63dff2d26b8ac59f46f3c Mon Sep 17 00:00:00 2001 From: Michael Joseph Date: Thu, 6 Jun 2019 20:04:21 -0400 Subject: [PATCH 4/4] Update test_auto_EddyQuad.py --- nipype/interfaces/fsl/tests/test_auto_EddyQuad.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py index a0d5085fbb..3cc6da2027 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py @@ -36,7 +36,7 @@ def test_EddyQuad_inputs(): ), output_type=dict(), param_file=dict( - argstr='--eddyParams=%s', + argstr='--eddyParams %s', mandatory=True, ), slice_spec=dict(argstr='--slspec %s', ),