cmind.pipeline.cmind_struct_preprocess

Functions

cmind_struct_preprocess(output_dir, struct_nii) Structural volume preprocessing pipeline
cmind.pipeline.cmind_struct_preprocess.cmind_struct_preprocess(output_dir, struct_nii, T2_struct_nii=None, age_months=252, bet_thresh=0.4, bet_use_T2=False, oname_root='T1W', reupdate_bias_cor=True, resegment_using_N4mask=False, ANTS_bias_cmd=None, omit_segmentation=False, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]

Structural volume preprocessing pipeline

Parameters:

output_dir : directory

directory in which to store the output

struct_nii : str

filename of T1-weighted NIFTI or NIFTIGZ volume to process

T2_struct_nii : str, optional

if T2_struct_nii is specified it will be rigidly registered to struct_nii. Brain extraction will be run on T2_struct_nii instead

age_months : float, optional

subject age in months (used during cropping)

bet_thresh : float, optional

bet brain extraction threshold

bet_use_T2 : bool, optional

if True, brain extract via T2_struct_nii instead of struct_nii

oname_root : str, optional

output filename prefix

reupdate_bias_cor : bool, optional

rerun bias correction after brain extraction

resegment_using_N4mask : bool, optional

if True, after initial segmentation rerun N4 bias correction, weighted to the WM mask. Repeat segmentation on the newly bias corrected image.

ANTS_bias_cmd : str, optional

location of N4BiasFieldCorrection binary

omit_segmentation : bool, optional

if True, omit segmentation

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:

fname_head : str

filename of Bias corrected head

fname_brain : str

filename of Bias corrected after brain extraction

fname_brain_mask : str

filename of brain mask

WM_vol : str or None

filename of WM partial volume estimate

GM_vol : str or None

filename of GM partial volume estimate

CSF_vol : str or None

filename of CSF partial volume estimate

bias_field_vol : str

filename of the N4 bias correction field

fname2_head : str or None

if T2_struct_nii is input, this is the corresponding bias-corrected head

fname2_brain : str or None

if T2_struct_nii is input, this is the corresponding bias-corrected brain

See also

cmind_crop_robust.py, cmind_bias_correct.py, cmind_brain_extract.py, cmind_structural.py

Notes

This function is a wrapper that calls other structural processing routines in the following order:
  • cmind_crop_robust.py
  • cmind_bias_correct.py
  • cmind_brain_extract.py
  • cmind_structural.py (optional)