nipype.interfaces.freesurfer.longitudinal module¶
Provides interfaces to various longitudinal commands provided by freesurfer
FuseSegmentations¶
Bases: FSCommand
Wrapped executable:
mri_fuse_segmentations
.fuse segmentations together from multiple timepoints
Examples
>>> from nipype.interfaces.freesurfer import FuseSegmentations >>> fuse = FuseSegmentations() >>> fuse.inputs.subject_id = 'tp.long.A.template' >>> fuse.inputs.timepoints = ['tp1', 'tp2'] >>> fuse.inputs.out_file = 'aseg.fused.mgz' >>> fuse.inputs.in_segmentations = ['aseg.mgz', 'aseg.mgz'] >>> fuse.inputs.in_segmentations_noCC = ['aseg.mgz', 'aseg.mgz'] >>> fuse.inputs.in_norms = ['norm.mgz', 'norm.mgz', 'norm.mgz'] >>> fuse.cmdline 'mri_fuse_segmentations -n norm.mgz -a aseg.mgz -c aseg.mgz tp.long.A.template tp1 tp2'
- in_normsa list of items which are a pathlike object or string representing an existing file
- -n <filename>
name of norm file to use (default: norm.mgs) must include the corresponding norm file for all given timepoints as well as for the current subject.
Maps to a command-line argument:
-n %s
.- in_segmentationsa list of items which are a pathlike object or string representing an existing file
Name of aseg file to use (default: aseg.mgz) must include the aseg files for all the given timepoints. Maps to a command-line argument:
-a %s
.- in_segmentations_noCCa list of items which are a pathlike object or string representing an existing file
Name of aseg file w/o CC labels (default: aseg.auto_noCCseg.mgz) must include the corresponding file for all the given timepoints. Maps to a command-line argument:
-c %s
.- out_filea pathlike object or string representing a file
Output fused segmentation file.
- timepointsa list of items which are a string
Subject_ids or timepoints to be processed. Maps to a command-line argument:
%s
(position: -2).
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- 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:
{}
)- subject_ida string
Subject_id being processed. Maps to a command-line argument:
%s
(position: -3).- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing a file
Output fused segmentation file.
RobustTemplate¶
Bases: FSCommandOpenMP
Wrapped executable:
mri_robust_template
.construct an unbiased robust template for longitudinal volumes
Examples
>>> from nipype.interfaces.freesurfer import RobustTemplate >>> template = RobustTemplate() >>> template.inputs.in_files = ['structural.nii', 'functional.nii'] >>> template.inputs.auto_detect_sensitivity = True >>> template.inputs.average_metric = 'mean' >>> template.inputs.initial_timepoint = 1 >>> template.inputs.fixed_timepoint = True >>> template.inputs.no_iteration = True >>> template.inputs.subsample_threshold = 200 >>> template.cmdline #doctest: 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template mri_robust_template_out.mgz --subsample 200' >>> template.inputs.out_file = 'T1.nii' >>> template.cmdline #doctest: 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --subsample 200'>>> template.inputs.transform_outputs = ['structural.lta', ... 'functional.lta'] >>> template.inputs.scaled_intensity_outputs = ['structural-iscale.txt', ... 'functional-iscale.txt'] >>> template.cmdline 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --iscaleout .../structural-iscale.txt .../functional-iscale.txt --subsample 200 --lta .../structural.lta .../functional.lta'>>> template.inputs.transform_outputs = True >>> template.inputs.scaled_intensity_outputs = True >>> template.cmdline 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --iscaleout .../is1.txt .../is2.txt --subsample 200 --lta .../tp1.lta .../tp2.lta'>>> template.run()References
[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template]
- auto_detect_sensitivitya boolean
Auto-detect good sensitivity (recommended for head or full brain scans). Maps to a command-line argument:
--satit
. Mutually exclusive with inputs:outlier_sensitivity
.- in_filesa list of items which are a pathlike object or string representing an existing file
Input movable volumes to be aligned to common mean/median template. Maps to a command-line argument:
--mov %s
.- out_filea pathlike object or string representing a file
Output template volume (final mean/median image). Maps to a command-line argument:
--template %s
. (Nipype default value:mri_robust_template_out.mgz
)- outlier_sensitivitya float
Set outlier sensitivity manually (e.g. “–sat 4.685” ). Higher values mean less sensitivity. Maps to a command-line argument:
--sat %.4f
. Mutually exclusive with inputs:auto_detect_sensitivity
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- average_metric‘median’ or ‘mean’
Construct template from: 0 Mean, 1 Median (default). Maps to a command-line argument:
--average %d
.- 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:
{}
)- fixed_timepointa boolean
Map everthing to init TP# (init TP is not resampled). Maps to a command-line argument:
--fixtp
.- in_intensity_scalesa list of items which are a pathlike object or string representing an existing file
Use initial intensity scales. Maps to a command-line argument:
--iscalein %s
.- initial_timepointan integer (int or long)
Use TP# for spacial init (default random), 0: no init. Maps to a command-line argument:
--inittp %d
.- initial_transformsa list of items which are a pathlike object or string representing an existing file
Use initial transforms (lta) on source. Maps to a command-line argument:
--ixforms %s
.- intensity_scalinga boolean
Allow also intensity scaling (default off). Maps to a command-line argument:
--iscale
.- no_iterationa boolean
Do not iterate, just create first template. Maps to a command-line argument:
--noit
.- num_threadsan integer (int or long)
Allows for specifying more threads.
- scaled_intensity_outputsa list of items which are a pathlike object or string representing a file or a boolean
Final intensity scales (will activate –iscale). Maps to a command-line argument:
--iscaleout %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- subsample_thresholdan integer (int or long)
Subsample if dim > # on all axes (default no subs.). Maps to a command-line argument:
--subsample %d
.- transform_outputsa list of items which are a pathlike object or string representing a file or a boolean
Output xforms to template (for each input). Maps to a command-line argument:
--lta %s
.
- out_filea pathlike object or string representing an existing file
Output template volume (final mean/median image).
- scaled_intensity_outputsa list of items which are a pathlike object or string representing an existing file
Output final intensity scales.
- transform_outputsa list of items which are a pathlike object or string representing an existing file
Output xform files from moving to template.