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)
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

cmind.pipeline.cmind_atlas_to_subject.split_atlas_outputs(Atlas_out)[source]