ENH: Add MultiChannelNewSegment interface

jhuguetn · jhuguetn · commit 2d1e327fb8ef · 2020-02-05T18:56:06.000+01:00
diff --git a/nipype/interfaces/spm/__init__.py b/nipype/interfaces/spm/__init__.py
@@ -14,6 +14,7 @@
     Segment,
     Smooth,
     NewSegment,
+    MultiChannelNewSegment,
     DARTEL,
     DARTELNorm2MNI,
     CreateWarped,
diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py
@@ -1865,6 +1865,262 @@ def _list_outputs(self):
         return outputs
 
 
+class MultiChannelNewSegmentInputSpec(SPMCommandInputSpec):
+    channels = traits.List(
+        traits.Tuple(
+            InputMultiPath(
+                ImageFileSPM(exists=True),
+                mandatory=True,
+                desc="A list of files to be segmented",
+                field="channel",
+                copyfile=False,
+            ),
+            traits.Tuple(
+                traits.Float(),
+                traits.Float(),
+                traits.Tuple(traits.Bool, traits.Bool),
+                desc="""A tuple with the following fields:
+                    - bias reguralisation (0-10)
+                    - FWHM of Gaussian smoothness of bias
+                    - which maps to save (Field, Corrected) - a tuple of two boolean values""",
+                field="channel",
+            )
+        ),
+        desc="""A list of tuples (one per each channel) with the following fields:
+            - a list of channel files (only 1rst channel files will be segmented)
+            - a tuple with the following channel-specific info fields:
+              - bias reguralisation (0-10)
+              - FWHM of Gaussian smoothness of bias
+              - which maps to save (Field, Corrected) - a tuple of two boolean values""",
+        field="channel",
+    )
+    tissues = traits.List(
+        traits.Tuple(
+            traits.Tuple(ImageFileSPM(exists=True), traits.Int()),
+            traits.Int(),
+            traits.Tuple(traits.Bool, traits.Bool),
+            traits.Tuple(traits.Bool, traits.Bool),
+        ),
+        desc="""A list of tuples (one per tissue) with the following fields:
+            - tissue probability map (4D), 1-based index to frame
+            - number of gaussians
+            - which maps to save [Native, DARTEL] - a tuple of two boolean values
+            - which maps to save [Unmodulated, Modulated] - a tuple of two boolean values""",
+        field="tissue",
+    )
+    affine_regularization = traits.Enum(
+        "mni",
+        "eastern",
+        "subj",
+        "none",
+        field="warp.affreg",
+        desc="mni, eastern, subj, none ",
+    )
+    warping_regularization = traits.Either(
+        traits.List(traits.Float(), minlen=5, maxlen=5),
+        traits.Float(),
+        field="warp.reg",
+        desc=(
+            "Warping regularization "
+            "parameter(s). Accepts float "
+            "or list of floats (the "
+            "latter is required by "
+            "SPM12)"
+        ),
+    )
+    sampling_distance = traits.Float(
+        field="warp.samp", desc=("Sampling distance on data for parameter estimation"),
+    )
+    write_deformation_fields = traits.List(
+        traits.Bool(),
+        minlen=2,
+        maxlen=2,
+        field="warp.write",
+        desc=("Which deformation fields to write:[Inverse, Forward]"),
+    )
+
+
+class MultiChannelNewSegmentOutputSpec(TraitedSpec):
+    native_class_images = traits.List(
+        traits.List(File(exists=True)), desc="native space probability maps"
+    )
+    dartel_input_images = traits.List(
+        traits.List(File(exists=True)), desc="dartel imported class images"
+    )
+    normalized_class_images = traits.List(
+        traits.List(File(exists=True)), desc="normalized class images"
+    )
+    modulated_class_images = traits.List(
+        traits.List(File(exists=True)), desc=("modulated+normalized class images")
+    )
+    transformation_mat = OutputMultiPath(
+        File(exists=True), desc="Normalization transformation"
+    )
+    bias_corrected_images = OutputMultiPath(
+        File(exists=True), desc="bias corrected images"
+    )
+    bias_field_images = OutputMultiPath(File(exists=True), desc="bias field images")
+    forward_deformation_field = OutputMultiPath(File(exists=True))
+    inverse_deformation_field = OutputMultiPath(File(exists=True))
+
+
+class MultiChannelNewSegment(SPMCommand):
+    """Use spm_preproc8 (New Segment) to separate structural images into
+    different tissue classes. Supports multiple modalities and multichannel inputs.
+
+    http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=45
+
+    Examples
+    --------
+    >>> import nipype.interfaces.spm as spm
+    >>> seg = spm.MultiChannelNewSegment()
+    >>> seg.inputs.channels = [('structural.nii',(0.0001, 60, (True, True)))]
+    >>> seg.run() # doctest: +SKIP
+
+    For VBM pre-processing [http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf],
+    TPM.nii should be replaced by /path/to/spm8/toolbox/Seg/TPM.nii
+
+    >>> seg = MultiChannelNewSegment()
+    >>> channel1= ('T1.nii',(0.0001, 60, (True, True)))
+    >>> channel2= ('T2.nii',(0.0001, 60, (True, True)))
+    >>> seg.inputs.channels = [channel1, channel2]
+    >>> tissue1 = (('TPM.nii', 1), 2, (True,True), (False, False))
+    >>> tissue2 = (('TPM.nii', 2), 2, (True,True), (False, False))
+    >>> tissue3 = (('TPM.nii', 3), 2, (True,False), (False, False))
+    >>> tissue4 = (('TPM.nii', 4), 2, (False,False), (False, False))
+    >>> tissue5 = (('TPM.nii', 5), 2, (False,False), (False, False))
+    >>> seg.inputs.tissues = [tissue1, tissue2, tissue3, tissue4, tissue5]
+    >>> seg.run() # doctest: +SKIP
+
+    """
+
+    input_spec = MultiChannelNewSegmentInputSpec
+    output_spec = MultiChannelNewSegmentOutputSpec
+
+    def __init__(self, **inputs):
+        _local_version = SPMCommand().version
+        if _local_version and "12." in _local_version:
+            self._jobtype = "spatial"
+            self._jobname = "preproc"
+        else:
+            self._jobtype = "tools"
+            self._jobname = "preproc8"
+
+        SPMCommand.__init__(self, **inputs)
+
+    def _format_arg(self, opt, spec, val):
+        """Convert input to appropriate format for spm
+        """
+
+        if opt == "channels":
+            # structure have to be recreated because of some weird traits error
+            new_channels = []
+            for channel in val:
+                new_channel = {}
+                new_channel["vols"] = scans_for_fnames(channel[0])
+                if isdefined(channel[1]):
+                    info = channel[1]
+                    new_channel["biasreg"] = info[0]
+                    new_channel["biasfwhm"] = info[1]
+                    new_channel["write"] = [int(info[2][0]), int(info[2][1])]
+                new_channels.append(new_channel)
+            return new_channels
+        elif opt == "tissues":
+            new_tissues = []
+            for tissue in val:
+                new_tissue = {}
+                new_tissue["tpm"] = np.array(
+                    [",".join([tissue[0][0], str(tissue[0][1])])], dtype=object
+                )
+                new_tissue["ngaus"] = tissue[1]
+                new_tissue["native"] = [int(tissue[2][0]), int(tissue[2][1])]
+                new_tissue["warped"] = [int(tissue[3][0]), int(tissue[3][1])]
+                new_tissues.append(new_tissue)
+            return new_tissues
+        elif opt == "write_deformation_fields":
+            return super(MultiChannelNewSegment, self)._format_arg(
+                opt, spec, [int(val[0]), int(val[1])]
+            )
+        else:
+            return super(MultiChannelNewSegment, self)._format_arg(opt, spec, val)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs["native_class_images"] = []
+        outputs["dartel_input_images"] = []
+        outputs["normalized_class_images"] = []
+        outputs["modulated_class_images"] = []
+        outputs["transformation_mat"] = []
+        outputs["bias_corrected_images"] = []
+        outputs["bias_field_images"] = []
+        outputs["inverse_deformation_field"] = []
+        outputs["forward_deformation_field"] = []
+
+        n_classes = 5
+        if isdefined(self.inputs.tissues):
+            n_classes = len(self.inputs.tissues)
+        for i in range(n_classes):
+            outputs["native_class_images"].append([])
+            outputs["dartel_input_images"].append([])
+            outputs["normalized_class_images"].append([])
+            outputs["modulated_class_images"].append([])
+
+        # main outputs are generated for the first channel images only
+        for filename in self.inputs.channels[0][0]:
+            pth, base, ext = split_filename(filename)
+            if isdefined(self.inputs.tissues):
+                for i, tissue in enumerate(self.inputs.tissues):
+                    if tissue[2][0]:
+                        outputs["native_class_images"][i].append(
+                            os.path.join(pth, "c%d%s.nii" % (i + 1, base))
+                        )
+                    if tissue[2][1]:
+                        outputs["dartel_input_images"][i].append(
+                            os.path.join(pth, "rc%d%s.nii" % (i + 1, base))
+                        )
+                    if tissue[3][0]:
+                        outputs["normalized_class_images"][i].append(
+                            os.path.join(pth, "wc%d%s.nii" % (i + 1, base))
+                        )
+                    if tissue[3][1]:
+                        outputs["modulated_class_images"][i].append(
+                            os.path.join(pth, "mwc%d%s.nii" % (i + 1, base))
+                        )
+            else:
+                for i in range(n_classes):
+                    outputs["native_class_images"][i].append(
+                        os.path.join(pth, "c%d%s.nii" % (i + 1, base))
+                    )
+            outputs["transformation_mat"].append(
+                os.path.join(pth, "%s_seg8.mat" % base)
+            )
+
+            if isdefined(self.inputs.write_deformation_fields):
+                if self.inputs.write_deformation_fields[0]:
+                    outputs["inverse_deformation_field"].append(
+                        os.path.join(pth, "iy_%s.nii" % base)
+                    )
+                if self.inputs.write_deformation_fields[1]:
+                    outputs["forward_deformation_field"].append(
+                        os.path.join(pth, "y_%s.nii" % base)
+                    )
+
+        # bias field related images are generated for images in all channels
+        for channel in self.inputs.channels:
+            for filename in channel[0]:
+                pth, base, ext = split_filename(filename)
+                if isdefined(channel[1]):
+                    if channel[1][2][0]:
+                        outputs["bias_field_images"].append(
+                            os.path.join(pth, "BiasField_%s.nii" % (base))
+                        )
+                    if channel[1][2][1]:
+                        outputs["bias_corrected_images"].append(
+                            os.path.join(pth, "m%s.nii" % (base))
+                        )
+        return outputs
+
+
 class SmoothInputSpec(SPMCommandInputSpec):
     in_files = InputMultiPath(
         ImageFileSPM(exists=True),
