cmind.pipeline.cmind_fMRI_norm

Functions

cmind_fMRI_norm(output_dir, reg_struct, ...) Apply previously computed transforms to normalize fMRI results to MNI
cmind.pipeline.cmind_fMRI_norm.cmind_fMRI_norm(output_dir, reg_struct, regBBR_dir, prep_dir, stats_dir, ANTS_path=None, reg_flag='001', output_tar=True, generate_figures=True, ForceUpdate=False, verbose=False, logger=None, update_reg_struct=False)[source]

Apply previously computed transforms to normalize fMRI results to MNI standard space

Parameters:

output_dir : str

directory in which to store the output

reg_struct : str or dict

filename of the .csv containing the registration structure

regBBR_dir : str

pathname to the BBR registration results (rigid from functional to structural)

prep_dir : str

directory containing the preprocessed fMRI volumes from cmind_fMRI_preprocess2

stats_dir : str

directory containing the first-level stats results

ANTS_path : str, optional

path to the ANTs binaries

reg_flag : str or int, optional

string of 3 characters controlling whether FLIRT, FNIRT and/or ANTS registrations of T1 to standard are to be run. doFLIRT = 0 or 1 (1 = do the regisration using FLIRT). doFNIRT = 0 or 1 (1 = do the regisration using FNIRT) (NOT CURRENTLY IMPLEMENTED). doANTS = 0, 1 or 2 (0 = skip, 1 = do using Exp, 2 = do using SyN)

output_tar : bool, optional

compress the registration folders into a .tar.gz archive

generate_figures : bool,optional

if true, generate overlay images summarizing the registration

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:

reg_tarfile : str

filename of the .tar.gz filenames corresponding to the lowres->highres registration results

reg_standard_tarfile : dict or str

dictionary containing the .tar.gz filenames corresponding to ‘FLIRT’, ‘FNIRT’, or ‘ANTS’ to MNI registration results. Will just be a str if only a single case was run.

reg_dir : str

directory containing highres registration

reg_standard_dir : str

directory containing standard space registration

Notes

To run a second level analysis, the /reg folder must have at least: highres.nii.gz, example_func2standard.mat If feat is being used for 2nd level analysis can remove tstat*.nii.gz from reg_standard/stats