8000 ENH: Update PETsurfer interface by mnoergaard · Pull Request #3602 · nipy/nipype · GitHub
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ENH: Update PETsurfer interface #3602

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Merged
merged 9 commits into from
Mar 20, 2024
Merged

ENH: Update PETsurfer interface #3602

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bd9d406
GTMPVC: add extra outputs to outputspec and GTMPVC class
mnoergaard Sep 8, 2023
ad5e559
FIX: update description of GTMPVC interface
mnoergaard Sep 8, 2023
f66b50f
ENH: update naming of MRTM interface to MRTM1 (more clear definition)
mnoergaard Sep 8, 2023
4df6a4b
ENH: update LoganRef interface to Logan (reference modeling is not us…
mnoergaard Sep 8, 2023
15eb049
ENH: add BP clipping arguments to mri_glmfit
mnoergaard Sep 8, 2023
0df01a7
formatted with black
bendhouseart Mar 19, 2024
ced00b1
Merge pull request #5 from bendhouseart/update_petsurfer
mnoergaard Mar 20, 2024
75f0ba0
TEST: Update tests
effigies Mar 20, 2024
6b7bda4
Merge remote-tracking branch 'upstream/master' into update_petsurfer
effigies Mar 20, 2024
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formatted with black
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@bendhouseart
bendhouseart committed Mar 19, 2024
commit 0df01a757dbd7af25ab05aad5d14ff8c236683c9
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")

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0