cmind.pipeline.cmind_atlas_to_subject¶
Functions
cmind_atlas_to_subject(output_dir, ...[, ...]) |
Transform a multi-label atlas from standard MNI standard space to subject space |
split_atlas_outputs(Atlas_out) |
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cmind.pipeline.cmind_atlas_to_subject.cmind_atlas_to_subject(output_dir, atlas_vol, ref_vol, reg_struct, ANTS_path=None, interp_type='NearestNeighbor', output_prefix='Atlas', split_script=None, omit_MNItoHR=False, HRtoLR_Affine=None, HRtoLR_Warp=None, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]¶ Transform a multi-label atlas from standard MNI standard space to subject space
Parameters: output_dir : str
directory in which to store the output
atlas_vol : str or list of str
filename of the NIFTI(GZ) format atlas
ref_vol : str
image filename for the “fixed” image (registration target)
reg_struct : str or dict
filename of the .csv file containing the registration dictionary
ANTS_path : str, optional
path to ANTs binaries
omit_MNItoHR : bool, optional
if True assume the atlas is already in structural space
interp_type : {‘NearestNeighbor’,’‘,’HammingWindowedSinc’,’BSpline[3]’}, optional
interpolation to use (should be nearest neighbor for binary atlases)
output_prefix : str or list of str, optional
prepend this string to the output filenames (default = ‘Atlas’)
split_script : str or None, optional
file name of the shell script that splits all masks within an atlas to separate volumes
HRtoLR_Affine : str or None, optional
affine transform from MNI standard space to functional space
HRtoLR_Warp : str or None, optional
fieldmap warp correction for transform from MNI standard space to functional space
generate_figures : bool, optional
if true, generate additional summary images
ForceUpdate : bool,optional
if True, rerun and overwrite any previously existing results
verbose : bool, optional
print additional output (to terminal and log)
logger : logging.Logger or str, optional
logging.Logger object (or string of a filename to log to)
Returns: Atlas_out : str or list of str
filename of the atlas in subject space
out1 : str
1st output
out2 : str or None
2jd output, if it exists
out3 : str or None
3rd output, if it exists
out4 : str or None
4th output, if it exists
out5 : str or None
5th output, if it exists
out6 : str or None
6th output, if it exists