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Fix nipy#3653 and nipy#3654 in the CAT12 Interface #3683

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Fix nipy#3653 and nipy#3654 in the CAT12 Interface #3683

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37d3ac2
Solved Issue #3654: added no surface measure (no ROI) option to cat12…
Jun 12, 2024
511ea71
FIX Issue #3654: added missing input traits for templates, corrected …
Jun 14, 2024
035bf8d
FIX #3653: added option for using compressed files as inputs in CAT12…
Jun 24, 2024
6afc8b5
Fix #3654: corrected if statement for saving ROI and ROIs files
Jul 1, 2024
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107 changes: 77 additions & 30 deletions nipype/interfaces/cat12/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
isdefined,
File,
Str,
ImageFile,
)
from nipype.interfaces.cat12.base import Cell

Expand All @@ -24,7 +25,7 @@

class CAT12SegmentInputSpec(SPMCommandInputSpec):
in_files = InputMultiPath(
ImageFileSPM(exists=True),
ImageFile(exists=True),
field="data",
desc="file to segment",
mandatory=True,
Expand Down Expand Up @@ -112,9 +113,9 @@
'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"
Expand Down Expand Up @@ -226,7 +227,7 @@
" 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,
Expand All @@ -239,33 +240,71 @@
neuromorphometrics = traits.Bool(
True,
field="output.ROImenu.atlases.neuromorphometrics",
usedefault=True,
# usedefault=True,
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We can't change the interface like this. The reason to have defaults expliciltly added is so that when tools change their defaults, old workflows that depended on those defaults would continue using the old settings.

If the changes are this extensive, new interfaces will be needed.

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),
field="output.ROImenu.atlases.ownatlas",
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
Expand Down Expand Up @@ -520,6 +559,8 @@
"""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)

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return scans_for_fnames(val)
else:
return scans_for_fname(val)
Expand All @@ -531,6 +572,8 @@
def _list_outputs(self):
outputs = self._outputs().get()
f = self.inputs.in_files[0]
if '.nii.gz' in f:
f = f[:-3]

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pth, base, ext = split_filename(f)

outputs["mri_images"] = [
Expand All @@ -554,22 +597,22 @@

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(

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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()
Expand All @@ -582,13 +625,17 @@
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(

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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(

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f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
)


return outputs

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