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Merged
merged 1 commit into from
Mar 20, 2024
Merged

formatted with black #5

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2 changes: 1 addition & 1 deletion nipype/interfaces/freesurfer/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,7 @@ class GLMFitInputSpec(FSTraitedSpec):
desc="RefTac TimeSec tstar : perform Logan kinetic modeling",
)
bp_clip_neg = traits.Bool(
argstr="--bp-clip-neg",
argstr="--bp-clip-neg",
desc="set negative BP voxels to zero",
)
bp_clip_max = traits.Float(
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11 changes: 8 additions & 3 deletions nipype/interfaces/freesurfer/petsurfer.py
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Expand Up @@ -460,7 +460,7 @@ class GTMPVCOutputSpec(TraitedSpec):
)
eres = File(
desc="4D PET file of residual error after PVC (smoothed with PSF)",
)
)
tissue_fraction = File(
desc="4D PET file of tissue fraction before PVC",
)
Expand All @@ -474,6 +474,7 @@ class GTMPVCOutputSpec(TraitedSpec):
desc="Color table file for segmentation file",
)


class GTMPVC(FSCommand):
"""Perform Partial Volume Correction (PVC) to PET Data.

Expand Down Expand Up @@ -551,8 +552,12 @@ def _list_outputs(self):
outputs["reg_pet2anat"] = os.path.join(pvcdir, "aux", "bbpet2anat.lta")
outputs["reg_anat2pet"] = os.path.join(pvcdir, "aux", "anat2bbpet.lta")
outputs["eres"] = os.path.join(pvcdir, "eres.nii.gz")
outputs["tissue_fraction"] = os.path.join(pvcdir, "aux", "tissue.fraction.nii.gz")
outputs["tissue_fraction_psf"] = os.path.join(pvcdir, "aux", "tissue.fraction.psf.nii.gz")
outputs["tissue_fraction"] = os.path.join(
pvcdir, "aux", "tissue.fraction.nii.gz"
)
outputs["tissue_fraction_psf"] = os.path.join(
pvcdir, "aux", "tissue.fraction.psf.nii.gz"
)
outputs["seg"] = os.path.join(pvcdir, "aux", "seg.nii.gz")
outputs["seg_ctab"] = os.path.join(pvcdir, "aux", "seg.ctab")

Expand Down