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FIX caching of afni allineate when out_matrix is specified #3141

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FIX caching of afni allineate when out_matrix is specified #3141

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7ef923a
generate out_matrix name
salma1601 Jan 4, 2020
2a1d705
update Allineate test
salma1601 Jan 4, 2020
7961a54
fix doctest
salma1601 Jan 5, 2020
5d68df6
split long line
salma1601 Jan 5, 2020
6c283dc
Merge remote-tracking branch 'upstream/master' into afni_allineate_ou…
effigies Feb 24, 2020
85aeffc
TEST: make specs
effigies Feb 24, 2020
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6 changes: 5 additions & 1 deletion nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -283,6 +283,9 @@ class AllineateInputSpec(AFNICommandInputSpec):
)
out_matrix = File(
argstr="-1Dmatrix_save %s",
name_template='%s_allineated.aff12.1D',
name_source='in_file',
keep_extension=False,
desc="Save the transformation matrix for each volume.",
xor=["in_matrix", "allcostx"],
)
Expand Down Expand Up @@ -576,7 +579,8 @@ class Allineate(AFNICommand):
>>> allineate.inputs.reference = 'structural.nii'
>>> allineate.inputs.nwarp_fixmot = ['X', 'Y']
>>> allineate.cmdline
'3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii'
'3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate \
-1Dmatrix_save functional_allineated.aff12 -base structural.nii'
>>> res = allineate.run() # doctest: +SKIP
"""

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7 changes: 6 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Allineate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,12 @@ def test_Allineate_inputs():
xor=["allcostx"],
),
out_matrix=dict(
argstr="-1Dmatrix_save %s", extensions=None, xor=["in_matrix", "allcostx"],
argstr="-1Dmatrix_save %s",
extensions=None,
keep_extension=False,
name_source="in_file",
name_template="%s_allineated.aff12.1D",
xor=["in_matrix", "allcostx"],
),
out_param_file=dict(
argstr="-1Dparam_save %s",
Expand Down