Home · Quickstart · User Guide and Examples · Interfaces Index · Developers · About · Nipy

# nipype.interfaces.workbench.metric module

This module provides interfaces for workbench surface commands

## MetricResample

Link to code

> Bases: WBCommand

> Wrapped executable: `wb_command -metric-resample`.

> 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`.

>     >>> from nipype.interfaces.workbench import MetricResample
>     >>> metres = MetricResample()
>     >>> metres.inputs.in_file = 'sub-01_task-rest_bold_space-fsaverage5.L.func.gii'
>     >>> metres.inputs.method = 'ADAP_BARY_AREA'
>     >>> metres.inputs.current_sphere = 'fsaverage5_std_sphere.L.10k_fsavg_L.surf.gii'
>     >>> metres.inputs.new_sphere = 'fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii'
>     >>> metres.inputs.area_metrics = True
>     >>> metres.inputs.current_area = 'fsaverage5.L.midthickness_va_avg.10k_fsavg_L.shape.gii'
>     >>> metres.inputs.new_area = 'fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii'
>     >>> metres.cmdline
>     'wb_command -metric-resample sub-01_task-rest_bold_space-fsaverage5.L.func.gii     fsaverage5_std_sphere.L.10k_fsavg_L.surf.gii     fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii     ADAP_BARY_AREA fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.out     -area-metrics fsaverage5.L.midthickness_va_avg.10k_fsavg_L.shape.gii     fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii'

> current_spherea pathlike object or string representing an existing file

>   A sphere surface with the mesh that the metric is currently on. Maps to a command-line argument: `%s` (position: 1).

> in_filea pathlike object or string representing an existing file

>   The metric file to resample. Maps to a command-line argument: `%s` (position: 0).

> method‘ADAP_BARY_AREA’ or ‘BARYCENTRIC’

>   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. Maps to a command-line argument: `%s` (position: 3).

> new_spherea pathlike object or string representing an existing file

>   A sphere surface that is in register with <current-sphere> and has the desired output mesh. Maps to a command-line argument: `%s` (position: 2).

> area_metricsa boolean

>   Specify vertex area metrics to do area correction based on. Maps to a command-line argument: `-area-metrics` (position: 5). Mutually exclusive with inputs: `area_surfs`.

> area_surfsa boolean

>   Specify surfaces to do vertex area correction based on. Maps to a command-line argument: `-area-surfs` (position: 5). Mutually exclusive with inputs: `area_metrics`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> current_areaa pathlike object or string representing an existing file

>   A relevant anatomical surface with <current-sphere> mesh OR a metric file with vertex areas for <current-sphere> mesh. Maps to a command-line argument: `%s` (position: 6).

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> largesta boolean

>   Use only the value of the vertex with the largest weight. Maps to a command-line argument: `-largest` (position: 10).

> new_areaa pathlike object or string representing an existing file

>   A relevant anatomical surface with <current-sphere> mesh OR a metric file with vertex areas for <current-sphere> mesh. Maps to a command-line argument: `%s` (position: 7).

> out_filea pathlike object or string representing a file

>   The output metric. Maps to a command-line argument: `%s` (position: 4).

> roi_metrica pathlike object or string representing an existing file

>   Input roi on the current mesh used to exclude non-data vertices. Maps to a command-line argument: `-current-roi %s` (position: 8).

> valid_roi_outa boolean

>   Output the ROI of vertices that got data from valid source vertices. Maps to a command-line argument: `-valid-roi-out` (position: 9).

> out_filea pathlike object or string representing an existing file

>   The output metric.

> roi_filea pathlike object or string representing a file

>   ROI of vertices that got data from valid source vertices.