caps.preclinic_functional.spm_preproc.SPMPreproc¶
SPMPreproc¶
- class caps.preclinic_functional.spm_preproc.SPMPreproc(autoexport_nodes_parameters=True, **kwargs)[source]¶
Inputs¶
[Mandatory]
register_to_mean: a boolean (mandatory)
Indicate whether realignment is done to the mean image
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[Optional]
bet_threshold: a float (optional)
fractional intensity threshold
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fwhm: a legal value (optional)
gaussian smoothing kernel width (mm)
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generate_binary_mask: a boolean (optional)
create binary mask image
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generate_mesh: a boolean (optional)
generate a vtk mesh brain surface
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generate_skull: a boolean (optional)
create skull image
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smooth_fwhm: a legal value or a float (optional)
3-list of fwhm for each dimension (opt)
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use_4d_input: a boolean (optional)
apply to 4D fMRI data
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Outputs¶
acquisition_time: a float
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bet_inskull_mask_file: a file name
path/name of inskull mask (if generated)
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bet_inskull_mesh_file: a file name
path/name of inskull mesh outline (if generated)
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bet_mask_file: a file name
path/name of binary brain mask (if generated)
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bet_meshfile: a file name
path/name of vtk mesh file (if generated)
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bet_out_file: a file name
path/name of skullstripped file (if generated)
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bet_outskin_mask_file: a file name
path/name of outskin mask (if generated)
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bet_outskin_mesh_file: a file name
path/name of outskin mesh outline (if generated)
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bet_outskull_mask_file: a file name
path/name of outskull mask (if generated)
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bet_outskull_mesh_file: a file name
path/name of outskull mesh outline (if generated)
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bet_skull_mask_file: a file name
path/name of skull mask (if generated)
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coregistered_image: a file name
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normalization_parameter: any value
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normalized_func_image: any value
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normalized_struct_image: any value
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number_of_slices: an integer
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realigned_time_series_image: a file name
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reference_mean_image: a file name
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repetition_time: a float
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slice_times: a legal value
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smoothed_image: a file name
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time_corrected_fmri_image: a file name
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Pipeline schema¶
