ENH: Add CAT12 interfaces #3310

mfmachado · 2021-03-09T12:07:06Z

Summary

Fixes #2783 .

List of changes proposed in this PR (pull-request)

Acknowledgment

(Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

…cat12 # Conflicts: # nipype/interfaces/cat12/surface.py

codecov · 2021-03-09T15:30:44Z

Codecov Report

Merging #3310 (16f62fc) into master (12d06fd) will increase coverage by 0.03%.
The diff coverage is 70.90%.

@@            Coverage Diff             @@
##           master    #3310      +/-   ##
==========================================
+ Coverage   65.01%   65.05%   +0.03%     
==========================================
  Files         302      306       +4     
  Lines       40035    40279     +244     
  Branches     5291     5320      +29     
==========================================
+ Hits        26029    26202     +173     
- Misses      12935    13006      +71     
  Partials     1071     1071

Flag	Coverage Δ
unittests	`64.82% <69.67%> (+0.02%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
nipype/interfaces/cat12/base.py	`45.45% <45.45%> (ø)`
nipype/interfaces/cat12/surface.py	`65.93% <65.93%> (ø)`
nipype/interfaces/cat12/preprocess.py	`75.71% <75.71%> (ø)`
nipype/interfaces/cat12/__init__.py	`100.00% <100.00%> (ø)`

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effigies

I had a look through preprocess.py, but haven't done the other yet. Don't forget to make specs.

effigies · 2021-03-31T14:17:39Z

nipype/interfaces/cat12/preprocess.py

+import traits
+from nipype.interfaces.base import InputMultiPath, TraitedSpec, isdefined


We use nipype.interfaces.base to override some aspects of traits. I would suggest the following:

Suggested change

import traits

from nipype.interfaces.base import InputMultiPath, TraitedSpec, isdefined

from nipype.interfaces.base import InputMultiPath, TraitedSpec, isdefined, traits, File, Str

Hi @effigies sorry for the late reply, I only had the time to correct you reviews today. I do not known what you mean by make specs...

effigies · 2021-03-31T14:20:31Z

nipype/interfaces/cat12/preprocess.py

+from traits.trait_types import Int, File
+from traits.trait_types import List


Suggested change

from traits.trait_types import Int, File

from traits.trait_types import List

effigies · 2021-03-31T14:21:07Z

nipype/interfaces/cat12/preprocess.py

+    """
+    CAT12: Segmentation
+    This toolbox is an extension to the default segmentation in SPM12, but uses a completely different segmentation
+    approach.
+    The segmentation approach is based on an Adaptive Maximum A Posterior (MAP) technique without the need for a priori
+    information about tissue probabilities. That is, the Tissue Probability Maps (TPM) are not used constantly in the
+    sense of the classical Unified Segmentation approach (Ashburner et. al. 2005), but just for spatial normalization.
+    The following AMAP estimation is adaptive in the sense that local variations of the parameters (i.e., means and
+    variance) are modeled as slowly varying spatial functions (Rajapakse et al. 1997). This not only accounts for
+    intensity inhomogeneities but also for other local variations of intensity.
+    Additionally, the segmentation approach uses a Partial Volume Estimation (PVE) with a simplified mixed model of at
+    most two tissue types (Tohka et al. 2004). We start with an initial segmentation into three pure classes: gray
+    matter (GM), white matter (WM), and cerebrospinal fluid (CSF) based on the above described AMAP estimation. The
+    initial segmentation is followed by a PVE of two additional mixed classes: GM-WM and GM-CSF. This results in an
+    estimation of the amount (or fraction) of each pure tissue type present in every voxel (as single voxels - given by
+    Another important extension to the SPM12 segmentation is the integration of the Dartel or Geodesic Shooting
+    registration into the toolbox by an already existing Dartel/Shooting template in MNI space. This template was
+    derived from 555 healthy control subjects of the IXI-database (http://www.brain-development.org) and provides the
+    several Dartel or Shooting iterations. Thus, for the majority of studies the creation of sample-specific templates
+    is not necessary anymore and is mainly recommended for children data.'};
+
+    http://www.neuro.uni-jena.de/cat12/CAT12-Manual.pdf#page=15
+
+    Examples
+    --------
+    >>> path_mr = 'structural.nii'
+    >>> cat = CAT12Segment(in_files=path_mr)
+    >>> cat.run() # doctest: +SKIP
+    """


This docstring should go on CAT12Segment, not CAT12SegmentInputSpec.

effigies · 2021-03-31T14:23:19Z

nipype/interfaces/cat12/preprocess.py

+    help_tpm = 'Tissue Probability Map. Select the tissue probability image that includes 6 tissue probability ' \
+               'classes for (1) grey matter, (2) white matter, (3) cerebrospinal fluid, (4) bone, (5) non-brain soft ' \
+               'tissue, and (6) the background.  CAT uses the TPM only for the initial SPM segmentation.'
+    tpm = InputMultiPath(ImageFileSPM(exists=True), field="tpm", desc=help_tpm, mandatory=False,
+                         copyfile=False)


For variables that are not traits, we use _ as a prefix to mark them as private. This will help declutter tab-completion in IPython or similar environments.

Suggested change

help_tpm = 'Tissue Probability Map. Select the tissue probability image that includes 6 tissue probability ' \

'classes for (1) grey matter, (2) white matter, (3) cerebrospinal fluid, (4) bone, (5) non-brain soft ' \

'tissue, and (6) the background. CAT uses the TPM only for the initial SPM segmentation.'

tpm = InputMultiPath(ImageFileSPM(exists=True), field="tpm", desc=help_tpm, mandatory=False,

copyfile=False)

_help_tpm = 'Tissue Probability Map. Select the tissue probability image that includes 6 tissue probability ' \

'classes for (1) grey matter, (2) white matter, (3) cerebrospinal fluid, (4) bone, (5) non-brain soft ' \

'tissue, and (6) the background. CAT uses the TPM only for the initial SPM segmentation.'

tpm = InputMultiPath(ImageFileSPM(exists=True), field="tpm", desc=_help_tpm, mandatory=False,

copyfile=False)

And so on for other traits.

effigies · 2021-03-31T14:24:38Z

nipype/interfaces/cat12/preprocess.py

+    n_jobs = traits.trait_types.Int(1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads")
+    use_prior = traits.trait_types.Str(field="useprior", usedefault=True)


Based on changed imports:

Suggested change

n_jobs = traits.trait_types.Int(1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads")

use_prior = traits.trait_types.Str(field="useprior", usedefault=True)

n_jobs = traits.Int(1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads")

use_prior = Str(field="useprior", usedefault=True)

And can you add a description to use_prior?

effigies · 2021-03-31T14:32:51Z

nipype/interfaces/cat12/preprocess.py

+                    else:
+                        outputs[outfield] = fname_presuffix(f, prefix=prefix, suffix="_rigid")
+
+        if isdefined(self.inputs.save_bias_corrected) and self.inputs.save_bias_corrected:


Suggested change

if isdefined(self.inputs.save_bias_corrected) and self.inputs.save_bias_corrected:

if self.inputs.save_bias_corrected:

effigies · 2021-03-31T14:33:25Z

nipype/interfaces/cat12/preprocess.py

+        outputs["surface_files"] = [os.path.join(os.path.join(pth, "surf"), f) for f in
+                                    os.listdir(os.path.join(pth, "surf"))
+                                    if os.path.isfile(os.path.join(os.path.join(pth, "surf"), f))]


Suggested change

outputs["surface_files"] = [os.path.join(os.path.join(pth, "surf"), f) for f in

os.listdir(os.path.join(pth, "surf"))

if os.path.isfile(os.path.join(os.path.join(pth, "surf"), f))]

outputs["surface_files"] = [str(surf) for surf in Path(pth).glob("surf/*") if surf.is_file()]

effigies · 2021-03-31T14:34:06Z

nipype/interfaces/cat12/preprocess.py

+        for tidx, hemisphere in enumerate(["rh", "lh"]):
+            for idx, suffix in enumerate(["central", "sphere"]):


Unused indices.

Suggested change

for tidx, hemisphere in enumerate(["rh", "lh"]):

for idx, suffix in enumerate(["central", "sphere"]):

for hemisphere in ("rh", "lh"):

for suffix in ("central", "sphere"):

effigies · 2021-03-31T14:35:09Z

nipype/interfaces/cat12/preprocess.py

+        outputs["report_files"] = [os.path.join(os.path.join(pth, "report"), f) for f in
+                                   os.listdir(os.path.join(pth, "report"))
+                                   if os.path.isfile(os.path.join(os.path.join(pth, "report"), f))]


Suggested change

outputs["report_files"] = [os.path.join(os.path.join(pth, "report"), f) for f in

os.listdir(os.path.join(pth, "report"))

if os.path.isfile(os.path.join(os.path.join(pth, "report"), f))]

outputs["report_files"] = [str(report) for report in Path(pth).glob("report/*") if report.is_file()]

effigies · 2021-03-31T14:41:01Z

nipype/interfaces/cat12/preprocess.py

+        outputs["label_files"] = [os.path.join(os.path.join(pth, "label"), f) for f in
+                                  os.listdir(os.path.join(pth, "label"))
+                                  if os.path.isfile(os.path.join(os.path.join(pth, "label"), f))]


Suggested change

outputs["label_files"] = [os.path.join(os.path.join(pth, "label"), f) for f in

os.listdir(os.path.join(pth, "label"))

if os.path.isfile(os.path.join(os.path.join(pth, "label"), f))]

outputs["label_files"] = [str(label) for label in Path(pth).glob("label/*") if label.is_file()]

Update nipype/interfaces/cat12/surface.py

effigies · 2021-04-02T14:34:28Z

nipype/interfaces/cat12/preprocess.py

+                         copyfile=False)
+
+    n_jobs = traits.Int(1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads")
+    use_prior = Str(field="useprior", usedefault=True)


Missing descriptions for:

use_prior

surface_measures

neuromorphometrics

lpba40

cobra

hammers

save_bias_corrected

Unclear descriptions:

own_atlas

gm_output_*

wm_output_*

csf_output_*

label_* / output_labelnative

las_*

effigies · 2021-04-29T16:46:07Z

There's a Makefile with a specs entry:

nipype/Makefile

Lines 71 to 73 in 4e8f54d

    
           specs: 
        
           	@echo "Checking specs and autogenerating spec tests" 
        
           	env PYTHONPATH=".:$(PYTHONPATH)" $(PYTHON) tools/checkspecs.py

If you run make specs, it will auto-generate a test for your new interface. If you don't have make installed, you can just run python tools/checkspecs.py, as it does the same thing.

effigies · 2021-04-30T21:22:18Z

@mfmachado I went ahead and merged master, ran black and make specs on your PR to get it ready to finish. Are you good with it at this point? If so, I can aim to do a final review soon.

effigies

This is basically good to go. Some small comments, only.

effigies · 2021-04-30T23:08:36Z

nipype/interfaces/cat12/preprocess.py

+
+    def _format_arg(self, opt, spec, val):
+        """Convert input to appropriate format for spm"""
+        if opt in ["in_files"]:


Suggested change

if opt in ["in_files"]:

if opt == "in_files":

effigies · 2021-04-30T23:09:00Z

nipype/interfaces/cat12/preprocess.py

+            for idx, (image, prefix) in enumerate(
+                [("modulated", "mw"), ("dartel", "r"), ("native", "")]
+            ):


idx is unused.

Suggested change

for idx, (image, prefix) in enumerate(

[("modulated", "mw"), ("dartel", "r"), ("native", "")]

):

for image, prefix in (("modulated", "mw"), ("dartel", "r"), ("native", "")):

effigies · 2021-04-30T23:10:03Z

nipype/interfaces/cat12/preprocess.py

+                if isdefined(getattr(self.inputs, outtype)) and getattr(
+                    self.inputs, outtype
+                ):


Undefined is treated as False, so this can be simplified:

Suggested change

if isdefined(getattr(self.inputs, outtype)) and getattr(

self.inputs, outtype

):

if getattr(self.inputs, outtype):

effigies · 2021-04-30T23:13:38Z

nipype/interfaces/cat12/preprocess.py

+        outputs[f"report"] = fname_presuffix(
+            f, prefix=os.path.join("report", f"cat_"), suffix=".xml", use_ext=False


Nothing to interpolate with f-strings.

Suggested change

outputs[f"report"] = fname_presuffix(

f, prefix=os.path.join("report", f"cat_"), suffix=".xml", use_ext=False

outputs["report"] = fname_presuffix(

f, prefix=os.path.join("report", "cat_"), suffix=".xml", use_ext=False

effigies · 2021-04-30T23:13:51Z

nipype/interfaces/cat12/preprocess.py

+        ]
+
+        outputs["label_rois"] = fname_presuffix(
+            f, prefix=os.path.join("label", f"catROIs_"), suffix=".xml", use_ext=False


Suggested change

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

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

effigies · 2021-04-30T23:14:00Z

nipype/interfaces/cat12/preprocess.py

+            f, prefix=os.path.join("label", f"catROIs_"), suffix=".xml", use_ext=False
+        )
+        outputs["label_roi"] = fname_presuffix(
+            f, prefix=os.path.join("label", f"catROI_"), suffix=".xml", use_ext=False


Suggested change

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

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

effigies · 2021-04-30T23:16:24Z

nipype/interfaces/cat12/preprocess.py

+    _dartel_help = (
+        "This option is to export data into a form that can be used with DARTEL. The SPM default is to "
+        "only apply rigid body transformation. However, a more appropriate option is to apply affine "
+        "transformation, because the additional scaling of the images requires less deformations to "
+        "non-linearly register brains to the template."
+    )
+


Unused.

Suggested change

_dartel_help = (

"This option is to export data into a form that can be used with DARTEL. The SPM default is to "

"only apply rigid body transformation. However, a more appropriate option is to apply affine "

"transformation, because the additional scaling of the images requires less deformations to "

"non-linearly register brains to the template."

)

effigies · 2021-05-01T00:21:00Z

nipype/interfaces/cat12/surface.py

+            pth, base, ext = split_filename(filename)
+            # The first part of the filename is rh.central or lh.central
+            original_filename = base.split(".", 2)[-1]
+            for i, (extracted_parameter, parameter_name) in enumerate(names_outputs):


Unused index i.

Suggested change

for i, (extracted_parameter, parameter_name) in enumerate(names_outputs):

for extracted_parameter, parameter_name in names_outputs:

effigies · 2021-05-01T01:02:43Z

nipype/interfaces/cat12/surface.py

+from traits.trait_base import _Undefined
+
+from nipype.interfaces.base import File, InputMultiPath, TraitedSpec, traits


We have the isdefined function.

Suggested change

from traits.trait_base import _Undefined

from nipype.interfaces.base import File, InputMultiPath, TraitedSpec, traits

from nipype.interfaces.base import File, InputMultiPath, TraitedSpec, traits, isdefined

effigies · 2021-05-01T01:33:58Z

nipype/interfaces/cat12/surface.py

+                        name_hemisphere = hemisphere + "_" + parameter_name
+                        if isinstance(outputs[name_hemisphere], _Undefined):
+                            outputs[name_hemisphere] = []
+                        if isinstance(outputs[all_files_hemisphere], _Undefined):


Suggested change

if isinstance(outputs[all_files_hemisphere], _Undefined):

if not isdefined(outputs[all_files_hemisphere]):

effigies · 2021-05-26T17:17:57Z

@mfmachado I'm going to try to make a release in the next couple days. If you want to try to finish this off, I'd love to include it!

mfmachado · 2021-05-28T13:26:31Z

Hi @effigies,

I have been super busy in the last couple of weeks, when are you going to do the release? I can try to do it this weekend.

effigies · 2021-05-28T14:54:25Z

Happy to wait on this PR if you expect to get it in soon. If you're very busy, we can also release and wait on this until you have more time.

Improved code.

mfmachado · 2021-05-30T22:02:14Z

Hi @effigies thanks for you input :)
I updated the code and corrected a bug that I detected meanwhile regarding the TPM and Shooting template. I use this code regularly, so I hope it does not have bugs.

mfmachado · 2021-05-31T13:28:23Z

Hi @effigies all testes passed :D

effigies

Thanks! I did a few minor cleanups just to polish this off, rather than put you through another round of review. If you want to have a quick look, let me know if there's anything you disagree with. Otherwise, I'll plan to merge tomorrow.

mfmachado · 2021-06-01T09:17:51Z

hi, yes I agree with your changes :)

mfmachado added 11 commits March 1, 2021 15:21

Added cat12 interface.

533850b

Updated .zenodo.json.

eb80b27

Added interfaces to extract measures from the surface using CAT12.

f109163

Improved documentation of the surface measures extraction.

d8ca991

- Added examples to the segmentation.

c906740

Improved documentation.

2885499

Added outputs to ExtractROIBasedSurfaceMeasures interface.

98f118d

Added files to test the interfaces.

7713f78

Added files to test the interfaces.

44b8605

Minor fix

1bed8ed

Merge remote-tracking branch 'origin/interface/cat12' into interface/…

d18eb1e

…cat12 # Conflicts: # nipype/interfaces/cat12/surface.py

mfmachado changed the title ~~ENH (enhancement) Interface/cat12~~ [ENH] Interface/cat12 Mar 9, 2021

mfmachado marked this pull request as ready for review March 9, 2021 15:37

mfmachado changed the title ~~[ENH] Interface/cat12~~ ENH Interface/cat12 Mar 9, 2021

mfmachado changed the title ~~ENH Interface/cat12~~ ENH: Interface/cat12 Mar 9, 2021

mfmachado added 2 commits March 15, 2021 21:53

Bug fix in the output of ROIMeasures.

aa41da6

Bug fix bias corrected file.

dd152ee

effigies reviewed Mar 31, 2021

View reviewed changes

Update nipype/interfaces/cat12/preprocess.py

ea72f5e

Update nipype/interfaces/cat12/surface.py

mfmachado requested a review from effigies April 1, 2021 16:03

effigies reviewed Apr 2, 2021

View reviewed changes

Added more variable descriptions.

89d3059

effigies added 2 commits April 30, 2021 17:18

Merge remote-tracking branch 'upstream/master' into interface/cat12

285eb05

STY: black

04718ac

effigies changed the title ~~ENH: Interface/cat12~~ ENH: Add CAT12 interfaces Apr 30, 2021

effigies added this to the 1.6.0 milestone Apr 30, 2021

TEST: make specs

8a44b46

effigies force-pushed the interface/cat12 branch from 37facad to 8a44b46 Compare April 30, 2021 21:25

effigies reviewed May 1, 2021

View reviewed changes

effigies modified the milestones: 1.6.0, 1.6.1 May 1, 2021

effigies mentioned this pull request May 26, 2021

REL: 1.6.1 #3336

Merged

14 tasks

Correct TPM and dartel shooting template format;

e40fcb6

Improved code.

mfmachado added 3 commits May 30, 2021 23:48

Added format utils.

920b879

Merge branch 'master' into interface/cat12

4f2511f

Reformatted preprocess.py.

56a02f2

mfmachado and others added 5 commits May 31, 2021 16:29

Updated test_auto_CAT12Segment.py.

8a0ccae

DOC: Add CAT12 to interfaces list

cdcdba9

RF: Move format_utils to base

20629a0

ENH: Add cat12 interfaces to __init__

fc4f82d

DOC: Minor cleanups

16f62fc

effigies approved these changes Jun 1, 2021

View reviewed changes

effigies merged commit 337bbc9 into nipy:master Jun 1, 2021

JohannesWiesner mentioned this pull request Jun 24, 2021

Add option to install CAT12 ReproNim/neurodocker#407

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ENH: Add CAT12 interfaces #3310

ENH: Add CAT12 interfaces #3310

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		import traits
		from nipype.interfaces.base import InputMultiPath, TraitedSpec, isdefined

		from traits.trait_types import Int, File
		from traits.trait_types import List

		n_jobs = traits.trait_types.Int(1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads")
		use_prior = traits.trait_types.Str(field="useprior", usedefault=True)

	if isdefined(self.inputs.save_bias_corrected) and self.inputs.save_bias_corrected:
	if self.inputs.save_bias_corrected:

		for tidx, hemisphere in enumerate(["rh", "lh"]):
		for idx, suffix in enumerate(["central", "sphere"]):

		outputs[f"report"] = fname_presuffix(
		f, prefix=os.path.join("report", f"cat_"), suffix=".xml", use_ext=False

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

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

	for i, (extracted_parameter, parameter_name) in enumerate(names_outputs):
	for extracted_parameter, parameter_name in names_outputs:

		from traits.trait_base import _Undefined

		from nipype.interfaces.base import File, InputMultiPath, TraitedSpec, traits

	if isinstance(outputs[all_files_hemisphere], _Undefined):
	if not isdefined(outputs[all_files_hemisphere]):

ENH: Add CAT12 interfaces #3310

ENH: Add CAT12 interfaces #3310

Conversation

mfmachado commented Mar 9, 2021 • edited Loading

Summary

List of changes proposed in this PR (pull-request)

Acknowledgment

codecov bot commented Mar 9, 2021 • edited Loading

Codecov Report

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