From 37d3ac27a96f34650299996b2d739de3a0d9cf22 Mon Sep 17 00:00:00 2001
From: Oweda <jailan.oweda@zislrds0074.zi.local>
Date: Wed, 12 Jun 2024 17:18:47 +0200
Subject: [PATCH 1/4] Solved Issue #3654: added no surface measure (no ROI)
option to cat12 interface
---
nipype/interfaces/cat12/preprocess.py | 21 +++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py
index ebc436c674..e13e591f71 100644
--- a/nipype/interfaces/cat12/preprocess.py
+++ b/nipype/interfaces/cat12/preprocess.py
@@ -525,6 +525,13 @@ def _format_arg(self, opt, spec, val):
return scans_for_fname(val)
elif opt in ["tpm", "shooting_tpm"]:
return Cell2Str(val)
+
+ if opt == "surface_measures":
+ if not self.inputs.surface_measures:
+ self.inputs.neuromorphometrics = False
+ self.inputs.lpba40 = False
+ self.inputs.cobra = False
+ self.inputs.hammers = False
return super()._format_arg(opt, spec, val)
@@ -583,12 +590,14 @@ def _list_outputs(self):
str(label) for label in Path(pth).glob("label/*") if label.is_file()
]
- 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_measures:
+ outputs["label_rois"] = fname_presuffix(
+ f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
+ )
+ else:
+ outputs["label_roi"] = fname_presuffix(
+ f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
+ )
return outputs
From 511ea71058382f296e9d6ea88d6681c122d3cc45 Mon Sep 17 00:00:00 2001
From: Oweda <jailan.oweda@zislrds0074.zi.local>
Date: Fri, 14 Jun 2024 17:02:46 +0200
Subject: [PATCH 2/4] FIX Issue #3654: added missing input traits for
templates, corrected if statements for when no surface or ROI estimations are
desired
---
nipype/interfaces/cat12/preprocess.py | 92 ++++++++++++++++++---------
1 file changed, 62 insertions(+), 30 deletions(-)
diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py
index e13e591f71..a8d7405765 100644
--- a/nipype/interfaces/cat12/preprocess.py
+++ b/nipype/interfaces/cat12/preprocess.py
@@ -226,39 +226,73 @@ 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,
field="output.surf_measures",
- usedefault=True,
+ # usedefault=True,
desc="Extract surface measures",
+ # requires=["neuromorphometrics", "lpba40", "cobra", "hammers", "thalamus", "thalamic_nuclei", "suit", "ibsr"],
+ # xor=["noROI"],
)
# Templates
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.thalamaic_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 +300,12 @@ 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
@@ -525,13 +565,6 @@ def _format_arg(self, opt, spec, val):
return scans_for_fname(val)
elif opt in ["tpm", "shooting_tpm"]:
return Cell2Str(val)
-
- if opt == "surface_measures":
- if not self.inputs.surface_measures:
- self.inputs.neuromorphometrics = False
- self.inputs.lpba40 = False
- self.inputs.cobra = False
- self.inputs.hammers = False
return super()._format_arg(opt, spec, val)
@@ -561,22 +594,22 @@ 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()
@@ -590,11 +623,10 @@ def _list_outputs(self):
str(label) for label in Path(pth).glob("label/*") if label.is_file()
]
- if self.inputs.surface_measures:
+ if self.inputs.noROI:
outputs["label_rois"] = fname_presuffix(
f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
)
- else:
outputs["label_roi"] = fname_presuffix(
f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
)
From 035bf8d0979aa4af2ac96cd9a3088abe0f4d117c Mon Sep 17 00:00:00 2001
From: Oweda <jailan.oweda@zislrds0074.zi.local>
Date: Mon, 24 Jun 2024 13:44:31 +0200
Subject: [PATCH 3/4] FIX #3653: added option for using compressed files as
inputs in CAT12 interface
---
nipype/interfaces/cat12/preprocess.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py
index a8d7405765..96f608163b 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,
@@ -560,6 +561,8 @@ 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)
@@ -572,7 +575,8 @@ def _list_outputs(self):
outputs = self._outputs().get()
f = self.inputs.in_files[0]
pth, base, ext = split_filename(f)
-
+ if '.nii.gz' in f:
+ f = f[:-3]
outputs["mri_images"] = [
str(mri) for mri in Path(pth).glob("mri/*") if mri.is_file()
]
From 6afc8b5c0f468f060cb741f3596b4d22cc5e672c Mon Sep 17 00:00:00 2001
From: Oweda <jailan.oweda@zislrds0074.zi.local>
Date: Mon, 1 Jul 2024 16:13:30 +0200
Subject: [PATCH 4/4] Fix #3654: corrected if statement for saving ROI and ROIs
files
---
nipype/interfaces/cat12/preprocess.py | 44 ++++++++++++++-------------
1 file changed, 23 insertions(+), 21 deletions(-)
diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py
index 96f608163b..7f20e3211c 100644
--- a/nipype/interfaces/cat12/preprocess.py
+++ b/nipype/interfaces/cat12/preprocess.py
@@ -113,9 +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"
@@ -232,10 +232,8 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
surface_measures = traits.Int(
1,
field="output.surf_measures",
- # usedefault=True,
+ usedefault=True,
desc="Extract surface measures",
- # requires=["neuromorphometrics", "lpba40", "cobra", "hammers", "thalamus", "thalamic_nuclei", "suit", "ibsr"],
- # xor=["noROI"],
)
# Templates
@@ -244,56 +242,56 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
field="output.ROImenu.atlases.neuromorphometrics",
# usedefault=True,
desc="Extract brain measures for Neuromorphometrics template",
- xor=["noROI"],
+ xor=["noROI"]
)
lpba40 = traits.Bool(
True,
field="output.ROImenu.atlases.lpba40",
# usedefault=True,
desc="Extract brain measures for LPBA40 template",
- xor=["noROI"],
+ xor=["noROI"]
)
cobra = traits.Bool(
True,
field="output.ROImenu.atlases.hammers",
# usedefault=True,
desc="Extract brain measures for COBRA template",
- xor=["noROI"],
+ xor=["noROI"]
)
hammers = traits.Bool(
False,
field="output.ROImenu.atlases.cobra",
# usedefault=True,
desc="Extract brain measures for Hammers template",
- xor=["noROI"],
+ xor=["noROI"]
)
thalamus = traits.Bool(
True,
field="output.ROImenu.atlases.thalamus",
# usedefault=True,
desc="Extract brain measures for Thalamus template",
- xor=["noROI"],
+ xor=["noROI"]
)
thalamic_nuclei = traits.Bool(
True,
- field="output.ROImenu.atlases.thalamaic_nuclei",
+ field="output.ROImenu.atlases.thalamic_nuclei",
# usedefault=True,
desc="Extract brain measures for Thalamic Nuclei template",
- xor=["noROI"],
+ xor=["noROI"]
)
suit = traits.Bool(
True,
field="output.ROImenu.atlases.suit",
# usedefault=True,
desc="Extract brain measures for Suit template",
- xor=["noROI"],
+ xor=["noROI"]
)
ibsr = traits.Bool(
False,
field="output.ROImenu.atlases.ibsr",
# usedefault=True,
desc="Extract brain measures for IBSR template",
- xor=["noROI"],
+ xor=["noROI"]
)
own_atlas = InputMultiPath(
ImageFileSPM(exists=True),
@@ -301,7 +299,7 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
desc="Extract brain measures for a given template",
mandatory=False,
copyfile=False,
- xor=["noROI"],
+ xor=["noROI"]
)
noROI = traits.Bool(
field="output.ROImenu.noROI",
@@ -574,9 +572,10 @@ def _format_arg(self, opt, spec, val):
def _list_outputs(self):
outputs = self._outputs().get()
f = self.inputs.in_files[0]
- pth, base, ext = split_filename(f)
if '.nii.gz' in f:
f = f[:-3]
+ pth, base, ext = split_filename(f)
+
outputs["mri_images"] = [
str(mri) for mri in Path(pth).glob("mri/*") if mri.is_file()
]
@@ -626,14 +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
+ )
- if self.inputs.noROI:
+ if self.inputs.surface_and_thickness_estimation:
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
- )
+
return outputs