interfaces.workbench.metric¶
MetricResample¶
Wraps the executable command 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'
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
The metric file to resample
argument: ``%s``, position: 0
current_sphere: (a pathlike object or string representing an existing
file)
A sphere surface with the mesh that the metric is currently on
argument: ``%s``, position: 1
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
argument: ``%s``, position: 2
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
argument: ``%s``, position: 3
[Optional]
out_file: (a pathlike object or string representing a file)
The output metric
argument: ``%s``, position: 4
area_surfs: (a boolean)
Specify surfaces to do vertex area correction based on
argument: ``-area-surfs``, position: 5
mutually_exclusive: area_metrics
area_metrics: (a boolean)
Specify vertex area metrics to do area correction based on
argument: ``-area-metrics``, position: 5
mutually_exclusive: area_surfs
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
argument: ``%s``, position: 6
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
argument: ``%s``, position: 7
roi_metric: (a pathlike object or string representing an existing
file)
Input roi on the current mesh used to exclude non-data vertices
argument: ``-current-roi %s``, position: 8
valid_roi_out: (a boolean)
Output the ROI of vertices that got data from valid source vertices
argument: ``-valid-roi-out``, position: 9
largest: (a boolean)
Use only the value of the vertex with the largest weight
argument: ``-largest``, position: 10
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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', nipype default value: {})
Environment variables
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