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ENH: Add option to exclude projecting high variance voxels to surface…
… (update of #2855) (#2956) Adds option --project-goodvoxels to address #2822. If enabled, voxels whose timeseries have locally high coefficient of variation, or which lie outside the cortex (based on signed distance volumes generated from the WM and pial surfaces), are excluded from volume-to-surface sampling of BOLD timeseries. Not enabled by default. - adds MetricDilate interface for Workbench's wb_command -metric-dilate, which, when using the --project-goodvoxels option, fills zero-value vertices in the BOLD surface timeseries by dilating in data from the nearest "good" (nonzero, nonempty) vertex.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,271 @@ | ||
| # -*- coding: utf-8 -*- | ||
| # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- | ||
| # vi: set ft=python sts=4 ts=4 sw=4 et: | ||
| """This module provides interfaces for workbench surface commands""" | ||
| import os | ||
|
|
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| from nipype import logging | ||
| from nipype.interfaces.base import CommandLineInputSpec, File, TraitedSpec, traits | ||
| from nipype.interfaces.workbench.base import WBCommand | ||
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| iflogger = logging.getLogger("nipype.interface") | ||
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| class MetricDilateInputSpec(CommandLineInputSpec): | ||
| in_file = File( | ||
| exists=True, | ||
| mandatory=True, | ||
| argstr="%s ", | ||
| position=0, | ||
| desc="the metric to dilate", | ||
| ) | ||
|
|
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| surf_file = File( | ||
| exists=True, | ||
| mandatory=True, | ||
| argstr="%s ", | ||
| position=1, | ||
| desc="the surface to compute on", | ||
| ) | ||
|
|
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| distance = traits.Float( | ||
| mandatory=True, | ||
| argstr="%f ", | ||
| position=2, | ||
| desc="distance in mm to dilate", | ||
| ) | ||
|
|
||
| out_file = File( | ||
| name_source=["in_file"], | ||
| name_template="%s.func.gii", | ||
| keep_extension=False, | ||
| argstr="%s ", | ||
| position=3, | ||
| desc="output - the output metric", | ||
| ) | ||
|
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||
| bad_vertex_roi_file = File( | ||
| argstr="-bad-vertex-roi %s ", | ||
| position=4, | ||
| desc="metric file, positive values denote vertices to have their values replaced", | ||
| ) | ||
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| data_roi_file = File( | ||
| argstr="-data-roi %s ", | ||
| position=5, | ||
| desc="metric file, positive values denote vertices that have data", | ||
| ) | ||
|
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||
| column = traits.Int( | ||
| position=6, | ||
| argstr="-column %d ", | ||
| desc="the column number", | ||
| ) | ||
|
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| nearest = traits.Bool( | ||
| position=7, | ||
| argstr="-nearest ", | ||
| desc="use the nearest good value instead of a weighted average", | ||
| ) | ||
|
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| linear = traits.Bool( | ||
| position=8, | ||
| argstr="-linear ", | ||
| desc="fill in values with linear interpolation along strongest gradient", | ||
| ) | ||
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| exponent = traits.Float( | ||
| argstr="-exponent %f ", | ||
| position=9, | ||
| default=6.0, | ||
| desc="exponent n to use in (area / (distance ^ n)) as the " | ||
| "weighting function (default 6)", | ||
| ) | ||
|
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| corrected_areas = File( | ||
| argstr="-corrected-areas %s ", | ||
| position=10, | ||
| desc="vertex areas to use instead of computing them from the surface", | ||
| ) | ||
|
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| legacy_cutoff = traits.Bool( | ||
| position=11, | ||
| argstr="-legacy-cutoff ", | ||
| desc="use the v1.3.2 method of choosing how many vertices to " | ||
| "use when calculating the dilated value with weighted method", | ||
| ) | ||
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| class MetricDilateOutputSpec(TraitedSpec): | ||
| out_file = File(exists=True, desc="output file") | ||
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| class MetricDilate(WBCommand): | ||
| """ | ||
| For all data values designated as bad, if they neighbor a good value or | ||
| are within the specified distance of a good value in the same kind of | ||
| model, replace the value with a distance weighted average of nearby good | ||
| values, otherwise set the value to zero. If -nearest is specified, it | ||
| will use the value from the closest good value within range instead of a | ||
| weighted average. When the input file contains label data, nearest | ||
| dilation is used on the surface, and weighted popularity is used in the | ||
| volume. | ||
| The -corrected-areas options are intended for dilating on group average | ||
| surfaces, but it is only an approximate correction for the reduction of | ||
| structure in a group average surface. | ||
| If -bad-vertex-roi is specified, all values, including those with | ||
| value zero, are good, except for locations with a positive value in the | ||
| ROI. If it is not specified, only values equal to zero are bad. | ||
| """ | ||
|
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| input_spec = MetricDilateInputSpec | ||
| output_spec = MetricDilateOutputSpec | ||
| _cmd = "wb_command -metric-dilate " | ||
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| class MetricResampleInputSpec(CommandLineInputSpec): | ||
| in_file = File( | ||
| exists=True, | ||
| mandatory=True, | ||
| argstr="%s", | ||
| position=0, | ||
| desc="The metric file to resample", | ||
| ) | ||
| current_sphere = File( | ||
| exists=True, | ||
| mandatory=True, | ||
| argstr="%s", | ||
| position=1, | ||
| desc="A sphere surface with the mesh that the metric is currently on", | ||
| ) | ||
| new_sphere = File( | ||
| exists=True, | ||
| mandatory=True, | ||
| argstr="%s", | ||
| position=2, | ||
| desc="A sphere surface that is in register with <current-sphere> and" | ||
| " has the desired output mesh", | ||
| ) | ||
| method = traits.Enum( | ||
| "ADAP_BARY_AREA", | ||
| "BARYCENTRIC", | ||
| argstr="%s", | ||
| mandatory=True, | ||
| position=3, | ||
| desc="The method name - ADAP_BARY_AREA method is recommended for" | ||
| " ordinary metric data, because it should use all data while" | ||
| " downsampling, unlike BARYCENTRIC. If ADAP_BARY_AREA is used," | ||
| " exactly one of area_surfs or area_metrics must be specified", | ||
| ) | ||
| out_file = File( | ||
| name_source=["new_sphere"], | ||
| name_template="%s.out", | ||
| keep_extension=True, | ||
| argstr="%s", | ||
| position=4, | ||
| desc="The output metric", | ||
| ) | ||
| area_surfs = traits.Bool( | ||
| position=5, | ||
| argstr="-area-surfs", | ||
| xor=["area_metrics"], | ||
| desc="Specify surfaces to do vertex area correction based on", | ||
| ) | ||
| area_metrics = traits.Bool( | ||
| position=5, | ||
| argstr="-area-metrics", | ||
| xor=["area_surfs"], | ||
| desc="Specify vertex area metrics to do area correction based on", | ||
| ) | ||
| current_area = File( | ||
| exists=True, | ||
| position=6, | ||
| argstr="%s", | ||
| desc="A relevant anatomical surface with <current-sphere> mesh OR" | ||
| " a metric file with vertex areas for <current-sphere> mesh", | ||
| ) | ||
| new_area = File( | ||
| exists=True, | ||
| position=7, | ||
| argstr="%s", | ||
| desc="A relevant anatomical surface with <current-sphere> mesh OR" | ||
| " a metric file with vertex areas for <current-sphere> mesh", | ||
| ) | ||
| roi_metric = File( | ||
| exists=True, | ||
| position=8, | ||
| argstr="-current-roi %s", | ||
| desc="Input roi on the current mesh used to exclude non-data vertices", | ||
| ) | ||
| valid_roi_out = traits.Bool( | ||
| position=9, | ||
| argstr="-valid-roi-out", | ||
| desc="Output the ROI of vertices that got data from valid source vertices", | ||
| ) | ||
| largest = traits.Bool( | ||
| position=10, | ||
| argstr="-largest", | ||
| desc="Use only the value of the vertex with the largest weight", | ||
| ) | ||
|
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|
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| class MetricResampleOutputSpec(TraitedSpec): | ||
| out_file = File(exists=True, desc="the output metric") | ||
| roi_file = File(desc="ROI of vertices that got data from valid source vertices") | ||
|
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|
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| class MetricResample(WBCommand): | ||
| """ | ||
| Resample a metric file to a different mesh | ||
| Resamples a metric file, given two spherical surfaces that are in | ||
| register. If ``ADAP_BARY_AREA`` is used, exactly one of -area-surfs or | ||
| ``-area-metrics`` must be specified. | ||
| The ``ADAP_BARY_AREA`` method is recommended for ordinary metric data, | ||
| because it should use all data while downsampling, unlike ``BARYCENTRIC``. | ||
| The recommended areas option for most data is individual midthicknesses | ||
| for individual data, and averaged vertex area metrics from individual | ||
| midthicknesses for group average data. | ||
| The ``-current-roi`` option only masks the input, the output may be slightly | ||
| dilated in comparison, consider using ``-metric-mask`` on the output when | ||
| using ``-current-roi``. | ||
| The ``-largest option`` results in nearest vertex behavior when used with | ||
| ``BARYCENTRIC``. When resampling a binary metric, consider thresholding at | ||
| 0.5 after resampling rather than using ``-largest``. | ||
| """ | ||
|
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| input_spec = MetricResampleInputSpec | ||
| output_spec = MetricResampleOutputSpec | ||
| _cmd = "wb_command -metric-resample" | ||
|
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| def _format_arg(self, opt, spec, val): | ||
| if opt in ["current_area", "new_area"]: | ||
| if not self.inputs.area_surfs and not self.inputs.area_metrics: | ||
| raise ValueError( | ||
| "{} was set but neither area_surfs or" " area_metrics were set".format(opt) | ||
| ) | ||
| if opt == "method": | ||
| if ( | ||
| val == "ADAP_BARY_AREA" | ||
| and not self.inputs.area_surfs | ||
| and not self.inputs.area_metrics | ||
| ): | ||
| raise ValueError("Exactly one of area_surfs or area_metrics" " must be specified") | ||
| if opt == "valid_roi_out" and val: | ||
| # generate a filename and add it to argstr | ||
| roi_out = self._gen_filename(self.inputs.in_file, suffix="_roi") | ||
| iflogger.info("Setting roi output file as", roi_out) | ||
| spec.argstr += " " + roi_out | ||
| return super(MetricResample, self)._format_arg(opt, spec, val) | ||
|
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| def _list_outputs(self): | ||
| outputs = super(MetricResample, self)._list_outputs() | ||
| if self.inputs.valid_roi_out: | ||
| roi_file = self._gen_filename(self.inputs.in_file, suffix="_roi") | ||
| outputs["roi_file"] = os.path.abspath(roi_file) | ||
| return outputs |
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