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Slicer _cmd revision and quotes around %s #3724

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Slicer _cmd revision and quotes around %s
andrewcyung Apr 25, 2025
bf97ba8
Merge branch 'master' into BRAINSresample-bugfix
andrewcyung Apr 29, 2025
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14 changes: 7 additions & 7 deletions nipype/interfaces/slicer/registration/brainsresample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,18 +12,18 @@


class BRAINSResampleInputSpec(CommandLineInputSpec):
inputVolume = File(desc="Image To Warp", exists=True, argstr="--inputVolume %s")
inputVolume = File(desc="Image To Warp", exists=True, argstr="--inputVolume \"%s\"")
referenceVolume = File(
desc="Reference image used only to define the output space. If not specified, the warping is done in the same space as the image to warp.",
exists=True,
argstr="--referenceVolume %s",
argstr="--referenceVolume \"%s\"",
)
outputVolume = traits.Either(
traits.Bool,
File(),
hash_files=False,
desc="Resulting deformed image",
argstr="--outputVolume %s",
argstr="--outputVolume \"%s\"",
)
pixelType = traits.Enum(
"float",
Expand All @@ -34,17 +34,17 @@ class BRAINSResampleInputSpec(CommandLineInputSpec):
"uchar",
"binary",
desc="Specifies the pixel type for the input/output images. The 'binary' pixel type uses a modified algorithm whereby the image is read in as unsigned char, a signed distance map is created, signed distance map is resampled, and then a thresholded image of type unsigned char is written to disk.",
argstr="--pixelType %s",
argstr="--pixelType \"%s\"",
)
deformationVolume = File(
desc="Displacement Field to be used to warp the image",
exists=True,
argstr="--deformationVolume %s",
argstr="--deformationVolume \"%s\"",
)
warpTransform = File(
desc="Filename for the BRAINSFit transform used in place of the deformation field",
exists=True,
argstr="--warpTransform %s",
argstr="--warpTransform \"%s\"",
)
interpolationMode = traits.Enum(
"NearestNeighbor",
Expand Down Expand Up @@ -103,5 +103,5 @@ class BRAINSResample(SEMLikeCommandLine):

input_spec = BRAINSResampleInputSpec
output_spec = BRAINSResampleOutputSpec
_cmd = "BRAINSResample "
_cmd = "Slicer --launch BRAINSResample "
_outputs_filenames = {"outputVolume": "outputVolume.nii"}