nipype.interfaces.workbench.metric module¶
This module provides interfaces for workbench surface commands
MetricResample¶
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, unlikeBARYCENTRIC
. 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 withBARYCENTRIC
. 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'
- Mandatory Inputs
current_sphere (a 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_file (a 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_sphere (a 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).- Optional Inputs
area_metrics (a 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_surfs (a 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
.args (a unicode string) – Additional parameters to the command. Maps to a command-line argument:
%s
.current_area (a 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).environ (a 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:
{}
)largest (a boolean) – Use only the value of the vertex with the largest weight. Maps to a command-line argument:
-largest
(position: 10).new_area (a 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_file (a pathlike object or string representing a file) – The output metric. Maps to a command-line argument:
%s
(position: 4).roi_metric (a 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_out (a boolean) – Output the ROI of vertices that got data from valid source vertices. Maps to a command-line argument:
-valid-roi-out
(position: 9).- Outputs
out_file (a pathlike object or string representing an existing file) – The output metric.
roi_file (a pathlike object or string representing a file) – ROI of vertices that got data from valid source vertices.