cmind.pipeline.cmind_T1_tissue_averages

Functions

cmind_T1_tissue_averages(output_dir, ...[, ...]) calculate average T1 value for each tissue type (GM, WM, CSF)
cmind.pipeline.cmind_T1_tissue_averages.cmind_T1_tissue_averages(output_dir, T1_map_file, NRMSE_file, GMpve, WMpve, CSFpve, CBF_quant_file=None, CBF_percent_file=None, HRtoCBF_affine=None, HRtoCBF_warp=None, PVEthresh_pct=75.0, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]

calculate average T1 value for each tissue type (GM, WM, CSF)

Parameters:

output_dir : str

directory in which to store the output

T1_map_file : str

image file containing the T1map fitting results

NRMSE_file : str

normalized root-mean-square error (NRMSE) image from T1_map fit

GMpve : str

GM partial volume estimate from structural processing

WMpve : str

WM partial volume estimate from structural processing

CSFpve : str

CSF partial volume estimate from structural processing

CBF_quant_file : str or None, optional

quantitative ASL image

CBF_percent_file : str or None, optional

ASL control-tag signal percentage image

HRtoCBF_affine : str or None, optional

affine transform: structural->BaselineCBF

HRtoCBF_warp : str or None, optional

warp: structural->BaselineCBF

PVEthresh_pct : float, optional

threshold PVE maps by this percentage. Valid range: (0 100]

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:

T1_avg_file : str

CBF_avg_file : str or None