cmind.pipeline.cmind_baselineCBF_quantitative¶
Functions
calcCBF_Wang2002 (deltaM, maskim, cbf_lambda, ...) |
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calcflash (a, TR, T1[, err]) |
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cmind_baselineCBF_quantify (output_dir, ...) |
Quantify CBF | ||
cmind_baselineCBF_quantitative (output_dir, ...) |
Quantify CBF |
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cmind.pipeline.cmind_baselineCBF_quantitative.
calcCBF_Wang2002
(deltaM, maskim, cbf_lambda, R1a, R1app, delta, delta_art, w, t, TR, alpha, M0_blood)[source]¶ Parameters: deltaM : ndarray
average (control-tag) ASL subtraction image
maskim : ndarray
boolean mask over which to perform the computation
cbf_lambda : float, optional
blood-brain partition coefficient
R1a : float
R1 relaxation rate of arterial blood (1/seconds)
R1app : float
apparent R1 relaxation rate (1/seconds)
delta : float
transit time (to capillary compartment) (seconds)
delta_art : float
arterial transit time (seconds)
w : float
post-labeling delay (seconds)
t : float
label duration (seconds)
TR : float
TR (seconds)
alpha : float
inversion efficiency
M0_blood : float
M0 of blood (usually estimated from WM or CSF)
Notes
Quantify CBF using the model of Wang et. al.
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cmind.pipeline.cmind_baselineCBF_quantitative.
calcflash
(a, TR, T1, err=0.01)[source]¶ Parameters: a : float
flip angle
TR : float
TR (ms)
T1 : float
T1 (ms) (should be in same time units as TR)
err : float
will calculate number of pulses needed to get within this amount of the steady state
Examples
(Source code, png, hires.png, pdf)
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cmind.pipeline.cmind_baselineCBF_quantitative.
cmind_baselineCBF_quantify
(output_dir, BaselineCBF_mcf_masked, N4BiasCBF, BaselineCBF_timepoints_kept, alpha_file, WMpve, T1_map_reg2CBF, alpha_const=0.75, HRtoLR_affine=None, HRtoLR_warp=None, relmot=None, relmot_thresh=1.5, cbf_lambda=0.9, R1a=0.625, delta=1.5, delta_art=1.3, w=1.4, tau=2.0, TR=4.0, T2star_wm=45.0, T2star_arterial_blood=53.0, TE=11.5, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)¶ Quantify CBF
Parameters: output_dir : str
directory in which to store the output
BaselineCBF_mcf_masked : str
masked, motion-corrected BaselineCBF volume
N4BiasCBF : str
BaselineCBF N4Bias field
BaselineCBF_timepoints_kept : str
Timepoints kept during BaselineCBF preprocessing
alpha_file : float or str
inversion efficiency or a text file containing the inversion efficiency
WMpve : str
white matter partial volume estimate
T1_map_reg2CBF : str or float, optional
T1map that has been registered to BaselineCBF_mcf_masked
alpha_const : float, optional
if alpha_file was specified, also repeat the CBF mapping using this value of alpha instead
HRtoLR_affine : str or None, optional
affine from highres (structural) to lowres space
HRtoLR_warp : str or None, optional
warp from highres (structural) to lowres space
relmot : str, optional
relative motion .rms file from mcflirt
relmot_thresh : float, optional
relative motion threshold (mm) for discarding timepoints
cbf_lambda : float, optional
blood-brain partition coefficient
R1a : float, optional
R1 relaxation rate of arterial blood (1/seconds)
delta : float, optional
transit time (to capillary compartment) (seconds)
delta_art : float, optional
arterial transit time (seconds)
w : float, optional
post-labeling delay (seconds)
tau : float, optional
label duration (seconds)
TR : float, optional
TR (seconds)
T2star_wm : float, optional
transverse relaxation rate of white matter
T2star_arterial_blood : float, optional
transverse relaxation rate of arterial blood
TE : float, optional
echo time of the ASL acquisition
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: CBF_Wang_file : str
filename of the quantitative CBF image using alpha from alpha_file
CBF_Wang_alphaconst_file : str
filename of the quantitative CBF image using alpha = alpha_const
Notes
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cmind.pipeline.cmind_baselineCBF_quantitative.
cmind_baselineCBF_quantitative
(output_dir, BaselineCBF_mcf_masked, N4BiasCBF, BaselineCBF_timepoints_kept, alpha_file, WMpve, T1_map_reg2CBF, alpha_const=0.75, HRtoLR_affine=None, HRtoLR_warp=None, relmot=None, relmot_thresh=1.5, cbf_lambda=0.9, R1a=0.625, delta=1.5, delta_art=1.3, w=1.4, tau=2.0, TR=4.0, T2star_wm=45.0, T2star_arterial_blood=53.0, TE=11.5, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]¶ Quantify CBF
Parameters: output_dir : str
directory in which to store the output
BaselineCBF_mcf_masked : str
masked, motion-corrected BaselineCBF volume
N4BiasCBF : str
BaselineCBF N4Bias field
BaselineCBF_timepoints_kept : str
Timepoints kept during BaselineCBF preprocessing
alpha_file : float or str
inversion efficiency or a text file containing the inversion efficiency
WMpve : str
white matter partial volume estimate
T1_map_reg2CBF : str or float, optional
T1map that has been registered to BaselineCBF_mcf_masked
alpha_const : float, optional
if alpha_file was specified, also repeat the CBF mapping using this value of alpha instead
HRtoLR_affine : str or None, optional
affine from highres (structural) to lowres space
HRtoLR_warp : str or None, optional
warp from highres (structural) to lowres space
relmot : str, optional
relative motion .rms file from mcflirt
relmot_thresh : float, optional
relative motion threshold (mm) for discarding timepoints
cbf_lambda : float, optional
blood-brain partition coefficient
R1a : float, optional
R1 relaxation rate of arterial blood (1/seconds)
delta : float, optional
transit time (to capillary compartment) (seconds)
delta_art : float, optional
arterial transit time (seconds)
w : float, optional
post-labeling delay (seconds)
tau : float, optional
label duration (seconds)
TR : float, optional
TR (seconds)
T2star_wm : float, optional
transverse relaxation rate of white matter
T2star_arterial_blood : float, optional
transverse relaxation rate of arterial blood
TE : float, optional
echo time of the ASL acquisition
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: CBF_Wang_file : str
filename of the quantitative CBF image using alpha from alpha_file
CBF_Wang_alphaconst_file : str
filename of the quantitative CBF image using alpha = alpha_const
Notes