diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py
index ebc436c674..7f20e3211c 100644
--- a/nipype/interfaces/cat12/preprocess.py
+++ b/nipype/interfaces/cat12/preprocess.py
@@ -9,6 +9,7 @@
isdefined,
File,
Str,
+ ImageFile,
)
from nipype.interfaces.cat12.base import Cell
@@ -24,7 +25,7 @@
class CAT12SegmentInputSpec(SPMCommandInputSpec):
in_files = InputMultiPath(
- ImageFileSPM(exists=True),
+ ImageFile(exists=True),
field="data",
desc="file to segment",
mandatory=True,
@@ -112,9 +113,9 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
'rhe "Optimized Shooting - superlarge ventricles" option for "Spatial registration" is ! '
"required Values: \nnone: 0;\nlight: 1;\nfull: 2;\ndefault: 1070."
)
- initial_segmentation = traits.Int(
- 0, field="extopts.spm_kamap", desc=_help_initial_seg, usedefault=True
- )
+ # initial_segmentation = traits.Int(
+ # 0, field="extopts.spm_kamap", desc=_help_initial_seg, usedefault=True
+ # )
_help_las = (
"Additionally to WM-inhomogeneities, GM intensity can vary across different regions such as the motor"
@@ -226,7 +227,7 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
" are not available as batch dependencies objects. "
)
surface_and_thickness_estimation = traits.Int(
- 1, field="surface", desc=_help_surf, usedefault=True
+ 1, field="output.surface", desc=_help_surf, usedefault=True
)
surface_measures = traits.Int(
1,
@@ -239,26 +240,58 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
neuromorphometrics = traits.Bool(
True,
field="output.ROImenu.atlases.neuromorphometrics",
- usedefault=True,
+ # usedefault=True,
desc="Extract brain measures for Neuromorphometrics template",
+ xor=["noROI"]
)
lpba40 = traits.Bool(
True,
field="output.ROImenu.atlases.lpba40",
- usedefault=True,
+ # usedefault=True,
desc="Extract brain measures for LPBA40 template",
+ xor=["noROI"]
)
cobra = traits.Bool(
True,
field="output.ROImenu.atlases.hammers",
- usedefault=True,
+ # usedefault=True,
desc="Extract brain measures for COBRA template",
+ xor=["noROI"]
)
hammers = traits.Bool(
- True,
+ False,
field="output.ROImenu.atlases.cobra",
- usedefault=True,
+ # usedefault=True,
desc="Extract brain measures for Hammers template",
+ xor=["noROI"]
+ )
+ thalamus = traits.Bool(
+ True,
+ field="output.ROImenu.atlases.thalamus",
+ # usedefault=True,
+ desc="Extract brain measures for Thalamus template",
+ xor=["noROI"]
+ )
+ thalamic_nuclei = traits.Bool(
+ True,
+ field="output.ROImenu.atlases.thalamic_nuclei",
+ # usedefault=True,
+ desc="Extract brain measures for Thalamic Nuclei template",
+ xor=["noROI"]
+ )
+ suit = traits.Bool(
+ True,
+ field="output.ROImenu.atlases.suit",
+ # usedefault=True,
+ desc="Extract brain measures for Suit template",
+ xor=["noROI"]
+ )
+ ibsr = traits.Bool(
+ False,
+ field="output.ROImenu.atlases.ibsr",
+ # usedefault=True,
+ desc="Extract brain measures for IBSR template",
+ xor=["noROI"]
)
own_atlas = InputMultiPath(
ImageFileSPM(exists=True),
@@ -266,6 +299,12 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
desc="Extract brain measures for a given template",
mandatory=False,
copyfile=False,
+ xor=["noROI"]
+ )
+ noROI = traits.Bool(
+ field="output.ROImenu.noROI",
+ desc="Select if no ROI analysis needed",
+ xor=["neuromorphometrics", "lpba40", "cobra", "hammers", "thalamus", "thalamic_nuclei", "suit", "ibsr"],
)
# Grey matter
@@ -520,6 +559,8 @@ def _format_arg(self, opt, spec, val):
"""Convert input to appropriate format for spm"""
if opt == "in_files":
if isinstance(val, list):
+ if '.nii.gz' in val[0]:
+ return scans_for_fnames(val, keep4d=True)
return scans_for_fnames(val)
else:
return scans_for_fname(val)
@@ -531,6 +572,8 @@ def _format_arg(self, opt, spec, val):
def _list_outputs(self):
outputs = self._outputs().get()
f = self.inputs.in_files[0]
+ if '.nii.gz' in f:
+ f = f[:-3]
pth, base, ext = split_filename(f)
outputs["mri_images"] = [
@@ -554,22 +597,22 @@ def _list_outputs(self):
if self.inputs.save_bias_corrected:
outputs["bias_corrected_image"] = fname_presuffix(
- f, prefix=os.path.join("mri", "wmi")
+ f, prefix=os.path.join("mri", "wm")
)
- outputs["surface_files"] = [
- str(surf) for surf in Path(pth).glob("surf/*") if surf.is_file()
- ]
-
- for hemisphere in ["rh", "lh"]:
- for suffix in ["central", "sphere"]:
- outfield = f"{hemisphere}_{suffix}_surface"
- outputs[outfield] = fname_presuffix(
- f,
- prefix=os.path.join("surf", f"{hemisphere}.{suffix}."),
- suffix=".gii",
- use_ext=False,
- )
+ if self.inputs.surface_and_thickness_estimation:
+ outputs["surface_files"] = [
+ str(surf) for surf in Path(pth).glob("surf/*") if surf.is_file()
+ ]
+ for hemisphere in ["rh", "lh"]:
+ for suffix in ["central", "sphere"]:
+ outfield = f"{hemisphere}_{suffix}_surface"
+ outputs[outfield] = fname_presuffix(
+ f,
+ prefix=os.path.join("surf", f"{hemisphere}.{suffix}."),
+ suffix=".gii",
+ use_ext=False,
+ )
outputs["report_files"] = outputs["report_files"] = [
str(report) for report in Path(pth).glob("report/*") if report.is_file()
@@ -582,13 +625,17 @@ def _list_outputs(self):
outputs["label_files"] = [
str(label) for label in Path(pth).glob("label/*") if label.is_file()
]
+
+ if self.inputs.neuromorphometrics or self.inputs.lpba40 or self.inputs.cobra or self.inputs.hammers or self.inputs.thalamus or self.inputs.thalamic_nuclei or self.inputs.suit or self.inputs.ibsr:
+ outputs["label_roi"] = fname_presuffix(
+ f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
+ )
- outputs["label_rois"] = fname_presuffix(
- f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
- )
- outputs["label_roi"] = fname_presuffix(
- f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
- )
+ if self.inputs.surface_and_thickness_estimation:
+ outputs["label_rois"] = fname_presuffix(
+ f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
+ )
+
return outputs