def groups(self, parser):
groups = []
group = IgnorableOptionGroup(parser,
"Registration",
ignore=self.ignore)
group.add_option(
"--regfrom",
help="Registration image (e.g. perfusion weighted image)",
type="image")
#group.add_option("--omat", help="Output file for transform matrix", default=None)
#group.add_option("--bbr", dest="do_bbr", help="Include BBR registration step using EPI_REG", action="store_true", default=False)
#group.add_option("--flirt", dest="do_flirt", help="Include rigid-body registration step using FLIRT", action="store_true", default=True)
#group.add_option("--flirtsch", help="user-specified FLIRT schedule for registration")
groups.append(group)
#group = IgnorableOptionGroup(parser, "Extra BBR registration refinement", ignore=self.ignore)
#group.add_option("-c", dest="cfile", help="ASL control/calibration image for initial registration - brain extracted")
#group.add_option("--wm_seg", dest="wm_seg", help="tissue segmenation image for bbr (in structural image space)")
#groups.append(group)
#group = IgnorableOptionGroup(parser, "Distortion correction using fieldmap (see epi_reg)", ignore=self.ignore)
#g.add_option("--nofmapreg", dest="nofmapreg", help="do not perform registration of fmap to T1 (use if fmap already registered)", action="store_true", default=False)
#groups.append(group)
#group = IgnorableOptionGroup(parser, "Deprecated", ignore=self.ignore)
#g.add_option("-r", dest="lowstruc", help="extra low resolution structural image - brain extracted")
#g.add_option("--inweight", dest="inweight", help="specify weights for input image - same functionality as the flirt -inweight option", type="float")
#groups.append(group)
return groups
def groups(self, parser):
groups = []
group = IgnorableOptionGroup(parser, "BASIL options", ignore=self.ignore)
group.add_option("--infertau", help="Infer bolus duration", action="store_true", default=False)
group.add_option("--inferart", help="Infer macro vascular (arterial) signal component (not supported for multi-TE data)", action="store_true", default=False)
group.add_option("--inferpc", help="Infer pre-capillary signal component (not supported for multi-TE data)", action="store_true", default=False)
group.add_option("--infert1", help="Include uncertainty in T1 values", action="store_true", default=False)
group.add_option("--infertexch", help="Infer exchange time (multi-TE data only)", action="store_true", default=False)
group.add_option("--artonly", help="Remove tissue component and infer only arterial component (not supported for multi-TE data)", action="store_true", default=False)
group.add_option("--fixbat", help="Fix bolus arrival time", action="store_false", default=True)
group.add_option("--batsd", help="Bolus arrival time standard deviation (s) - default 1.0 for multi-PLD, 0.1 otherwise", type=float)
group.add_option("--spatial", help="Add step that implements adaptive spatial smoothing on CBF", action="store_true", default=False)
group.add_option("--fast", help="Faster analysis (1=faster, 2=single step", type=int, default=0)
group.add_option("--noiseprior", help="Use an informative prior for the noise estimation", action="store_true", default=False)
group.add_option("--noisesd", help="Set a custom noise std. dev. for the nosie prior", type=float)
group.add_option("--basil-options", "--fit-options", help="File containing additional options for model fitting step", type="optfile")
groups.append(group)
group = IgnorableOptionGroup(parser, "Model options", ignore=self.ignore)
group.add_option("--disp", help="Model for label dispersion", default="none")
group.add_option("--exch", help="Model for tissue exchange (residue function)", default="mix")
groups.append(group)
group = IgnorableOptionGroup(parser, "Partial volume correction / CBF estimation (enforces --spatial)", ignore=self.ignore)
group.add_option("--pgm", help="Gray matter PV map", type="image")
group.add_option("--pwm", help="White matter PV map", type="image")
groups.append(group)
group = IgnorableOptionGroup(parser, "Special options", ignore=self.ignore)
group.add_option("--t1im", help="Voxelwise T1 tissue estimates", type="image")
group.add_option("--batim", "--attim", help="Voxelwise BAT (ATT) estimates in seconds", type="image")
groups.append(group)
return groups
def groups(self, parser):
group = IgnorableOptionGroup(parser, "ENABLE options", ignore=self.ignore)
group.add_option("--noise", "-n", dest="noise_roi", help="Noise ROI. If not specified, will run BET on structural image and invert the brain mask", type="image")
group.add_option("--noise-from-struc", help="If specified, noise ROI is assumed to be in structural image space and will be registered to ASL space", action="store_true", default=False)
group.add_option("--gm", dest="gm_roi", help="Grey matter ROI. If not specified, FAST will be run on the structural image", type="image")
group.add_option("--gm-from-struc", help="If specified, GM ROI is assumed to be in T1 image space and will be registered to ASL space", action="store_true", default=False)
group.add_option("--regfrom", help="Reference image in ASL space for registration and motion correction. If not specified will use middle volume of ASL data", type="image")
group.add_option("--min-nvols", help="Minimum number of repeats to keep for each TI", type="int", default=6)
return [group]
def groups(self, parser):
group = IgnorableOptionGroup(parser,
"Preprocessing",
ignore=self.ignore)
group.add_option("--diff",
help="Perform tag-control subtraction",
action="store_true",
default=False)
group.add_option("--smooth",
help="Spatially smooth data",
action="store_true",
default=False)
group.add_option("--fwhm",
help="FWHM for spatial filter kernel",
type="float",
default=6)
group.add_option("--mc",
help="Motion correct data",
action="store_true",
default=False)
group.add_option("--ref",
help="Optional reference image for motion correction",
type="image",
default=None)
group.add_option("--reorder", help="Re-order data in specified order")
return [
group,
]
def groups(self, parser):
ret = []
g = IgnorableOptionGroup(parser, "General Pipeline Options")
g.add_option(
"--wp",
help=
"Analysis which conforms to the 'white papers' (Alsop et al 2014)",
action="store_true",
default=False)
g.add_option("--mc",
help="Motion correct data",
action="store_true",
default=False)
if oxasl_enable:
g.add_option("--use-enable",
help="Use ENABLE preprocessing step",
action="store_true",
default=False)
ret.append(g)
g = IgnorableOptionGroup(parser, "Model fitting options")
g.add_option("--fixbat",
dest="inferbat",
help="Fix bolus arrival time",
action="store_false",
default=True)
g.add_option(
"--batsd",
help=
"Bolus arrival time standard deviation (s) - default 1.0 for multi-PLD, 0.1 otherwise",
type=float)
g.add_option("--fixbolus",
"--fixtau",
dest="infertau",
help="Fix bolus duration",
action="store_false")
g.add_option("--art-off",
"--artoff",
dest="inferart",
help="Do not infer arterial component",
action="store_false",
default=True)
g.add_option("--spatial-off",
"--spatialoff",
dest="spatial",
help="Do not include adaptive spatial smoothing on CBF",
action="store_false",
default=True)
g.add_option("--infertexch",
help="Infer exchange time (multi-TE data only)",
action="store_true",
default=False)
g.add_option("--infert1",
help="Infer T1 value",
action="store_true",
default=False)
g.add_option("--infert2",
help="Infer T2 value (multi-TE data only)",
action="store_true",
default=False)
g.add_option("--t1im",
help="Voxelwise T1 tissue estimates",
type="image")
g.add_option("--batim",
"--attim",
help="Voxelwise BAT (ATT) estimates in seconds",
type="image")
g.add_option(
"--basil-options",
"--fit-options",
help="File containing additional options for model fitting step",
type="optfile",
default=None)
ret.append(g)
g = IgnorableOptionGroup(
parser,
"Physiological parameters (all have default values from literature)"
)
g.add_option(
"--bat",
help=
"Estimated bolus arrival time (s) - default=0.7 (pASL), 1.3 (cASL)",
type=float)
g.add_option("--t1",
"--t1t",
help="Tissue T1 (s)",
type=float,
default=1.3)
g.add_option("--t2",
"--t2t",
help="Tissue T2 (ms)",
type=float,
default=50)
g.add_option("--t2s", help="Tissue T2* (ms)", type=float, default=20)
g.add_option("--t1b", help="Blood T1 (s)", type=float, default=1.65)
g.add_option(
"--t2b",
help=
"Blood T2 (ms) - Lu et al. 2012 MRM 67:42-49, 3T during normoxia",
type=float,
default=150)
g.add_option("--t2sb",
help="Blood T2* (ms) - Petersen 2006 MRM 55(2):219-232",
type=float,
default=50)
ret.append(g)
g = IgnorableOptionGroup(parser, "Output options")
g.add_option("--save-corrected",
help="Save corrected input data",
action="store_true",
default=False)
g.add_option("--save-reg",
help="Save registration information (transforms etc)",
action="store_true",
default=False)
g.add_option("--save-basil",
help="Save Basil modelling output",
action="store_true",
default=False)
g.add_option("--save-calib",
help="Save calibration output",
action="store_true",
default=False)
g.add_option("--save-all",
help="Save all output (enabled when --debug specified)",
action="store_true",
default=False)
g.add_option("--output-stddev",
"--output-std",
help="Output standard deviation of estimated variables",
action="store_true",
default=False)
g.add_option("--output-var",
"--vars",
help="Output variance of estimated variables",
action="store_true",
default=False)
g.add_option("--output-residuals",
help="Output residuals (model fit - actual data)",
action="store_true",
default=False)
g.add_option("--output-mni",
help="Output in MNI standard space",
action="store_true",
default=False)
g.add_option(
"--output-custom",
help=
"Output in custom space (provide path to reference image in space)",
type=str)
g.add_option(
"--output-custom-mat",
help=
"(Optional) FLIRT transformation from structural space to custom space. "
+
"If not provided, will FLIRT registration from structural to --output-custom will be used.",
type=str)
g.add_option("--no-report",
dest="save_report",
help="Don't try to generate an HTML report",
action="store_false",
default=True)
ret.append(g)
return ret
def groups(self, parser):
ret = []
g = IgnorableOptionGroup(parser,
"Distortion correction using fieldmap")
g.add_option("--fmap", help="fieldmap image (in rad/s)", type="image")
g.add_option("--fmapmag",
help="fieldmap magnitude image - wholehead extracted",
type="image")
g.add_option("--fmapmagbrain",
help="fieldmap magnitude image - brain extracted",
type="image")
g.add_option(
"--nofmapreg",
help=
"Do not perform registration of fmap to T1 (use if fmap already in T1-space)",
action="store_true",
default=False)
ret.append(g)
g = IgnorableOptionGroup(
parser,
"Distortion correction using phase-encode-reversed calibration image (TOPUP)"
)
g.add_option("--cblip",
help="phase-encode-reversed (blipped) calibration image",
type="image")
ret.append(g)
g = IgnorableOptionGroup(parser,
"General distortion correction options")
g.add_option(
"--echospacing",
help=
"Effective EPI echo spacing (sometimes called dwell time) - in seconds",
type=float)
g.add_option("--pedir",
help="Phase encoding direction, dir = x/y/z/-x/-y/-z")
g.add_option(
"--gdc-warp",
"--gdcwarp",
help=
"Additional warp image for gradient distortion correction - will be combined with fieldmap or TOPUP distortion correction",
type="image")
ret.append(g)
g = IgnorableOptionGroup(parser, "Sensitivity correction")
g.add_option("--cref",
help="Reference image for sensitivity correction",
type="image")
g.add_option(
"--cact",
help=
"Image from coil used for actual ASL acquisition (default: calibration image - only in longtr mode)",
type="image")
g.add_option("--isen",
help="User-supplied sensitivity correction in ASL space")
g.add_option(
"--senscorr-auto",
"--senscorr",
help=
"Apply automatic sensitivity correction using bias field from FAST",
action="store_true",
default=False)
g.add_option("--senscorr-off",
help="Do not apply any sensitivity correction",
action="store_true",
default=False)
ret.append(g)
g = IgnorableOptionGroup(parser, "Partial volume correction (PVEc)")
g.add_option(
"--pvcorr",
help="Apply PVEc using FAST estimates taken from --fslanat dir",
action="store_true",
default=False)
g.add_option(
"--surf-pvcorr",
help=
"Apply PVEc using surface PV estimates taken from --fslanat dir w/ surfaces (not mutually exclusive with --pvcorr)",
action="store_true",
default=False)
g.add_option('--cores',
help="Number of processor cores to use for --surf-pvcorr",
type=int)
g.add_option(
"--pvgm",
help=
"GM PV estimates in ASL space (apply PVEc only, don't estimate PVs)",
type="image",
default=None)
g.add_option("--pvwm",
help="As above, WM PV estimates in ASL space",
type="image",
default=None)
ret.append(g)
return ret
def groups(self, parser):
group = IgnorableOptionGroup(parser, self.title, ignore=self.ignore)
group.add_option("--struc", "-s", help="Structural image", type="image", default=None)
group.add_option("--struc-brain", "--sbet", "--struc-bet", type="image", help="Structural image (brain extracted)", default=None)
group.add_option("--struc2asl", help="Structural->ASL transformation matrix", default=None)
group.add_option("--asl2struc", help="ASL->Structural transformation matrix", default=None)
group.add_option("--wm-seg", help="White matter segmentation of structural image", type="image", default=None)
group.add_option("--gm-seg", help="Grey matter segmentation of structural image", type="image", default=None)
group.add_option("--csf-seg", help="CSF segmentation of structural image", type="image", default=None)
group.add_option("--fslanat", help="FSL_ANAT output directory for structural information", default=None)
group.add_option("--fastsrc", help="Images from a FAST segmentation - if not set FAST will be run on structural image")
group.add_option("--struc2std", help="Structural to MNI152 linear registration (.mat)")
group.add_option("--struc2std-warp", help="Structural to MNI152 non-linear registration (warp)")
return [group, ]
def groups(self, parser):
groups = []
group = IgnorableOptionGroup(parser, "Calibration", ignore=self.ignore)
group.add_option("--calib",
"-c",
help="Calibration image",
type="image")
group.add_option(
"--perf",
"-i",
help=
"Perfusion image for calibration, in same image space as calibration image",
type="image")
group.add_option("--calib-method",
"--cmethod",
help="Calibration method: voxelwise or refregion")
group.add_option("--calib-alpha",
"--alpha",
help="Inversion efficiency",
type=float,
default=None)
group.add_option("--calib-gain",
"--cgain",
help="Relative gain between calibration and ASL data",
type=float,
default=1.0)
group.add_option(
"--calib-aslreg",
help="Calibration image is already aligned with ASL image",
action="store_true",
default=False)
group.add_option("--tr",
help="TR used in calibration sequence (s)",
type=float,
default=3.2)
groups.append(group)
group = IgnorableOptionGroup(parser,
"Voxelwise calibration",
ignore=self.ignore)
group.add_option("--pct",
help="Tissue/arterial partition coefficiant",
type=float,
default=0.9)
groups.append(group)
group = IgnorableOptionGroup(parser,
"Reference region calibration",
ignore=self.ignore)
group.add_option("--mode",
help="Calibration mode (longtr or satrevoc)",
default="longtr")
group.add_option("--tissref",
help="Tissue reference type (csf, wm, gm or none)",
default="csf")
group.add_option("--te",
help="Sequence TE (ms)",
type=float,
default=0.0)
group.add_option(
"--refmask",
"--csf",
help="Reference tissue mask in calibration image space",
type="image")
group.add_option(
"--t1r",
help=
"T1 of reference tissue (s) - defaults: csf 4.3, gm 1.3, wm 1.0",
type=float,
default=None)
group.add_option(
"--t2r",
help=
"T2/T2* of reference tissue (ms) - defaults T2/T2*: csf 750/400, gm 100/60, wm 50/50",
type=float,
default=None)
group.add_option(
"--t2star",
action="store_true",
default=False,
help=
"Correct with T2* rather than T2 (alters the default T2 values)")
group.add_option(
"--pcr",
help=
"Reference tissue partition coefficiant (defaults csf 1.15, gm 0.98, wm 0.82)",
type=float,
default=None)
groups.append(group)
group = IgnorableOptionGroup(
parser,
"longtr mode (calibration image is a control image with a long TR)",
ignore=self.ignore)
groups.append(group)
group = IgnorableOptionGroup(
parser,
"satrecov mode (calibration image is a sequnce of control images at various TIs)",
ignore=self.ignore)
group.add_option(
"--tis",
help=
"Comma separated list of inversion times, e.group. --tis 0.2,0.4,0.6"
)
group.add_option(
"--fa",
help="Flip angle (in degrees) for Look-Locker readouts",
type=float)
group.add_option(
"--lfa",
help="Lower flip angle (in degrees) for dual FA calibration",
type=float)
group.add_option("--calib-nphases",
help="Number of phases (repetitions) of higher FA",
type=int)
group.add_option(
"--fixa",
action="store_true",
default=False,
help=
"Fix the saturation efficiency to 100% (useful if you have a low number of samples)"
)
groups.append(group)
#group = IgnorableOptionGroup(parser, "CSF masking options (only for --tissref csf)", ignore=self.ignore)
#group.add_option("--csfmaskingoff", action="store_true", default=False, help="Turn off the ventricle masking, reference is based on segmentation only.")
#group.add_option("--str2std", help="Structural to MNI152 linear registration (.mat)")
#group.add_option("--warp", help="Structural to MNI152 non-linear registration (warp)")
return groups
def groups(self, parser):
groups = []
group = IgnorableOptionGroup(parser,
"Multiphase Options",
ignore=self.ignore)
group.add_option(
"--mp-spatial",
help="Enable spatial smoothing on multiphase fitting step",
action="store_true",
default=False)
group.add_option(
"--mp-spatial-phase",
help=
"Perform spatial regularization on the phase rather than the magnitude",
action="store_true",
default=False)
group.add_option(
"--mp-options",
help=
"File containing additional options for multiphase fitting step",
type="optfile")
group.add_option(
"--mp-init-step",
help=
"Initialize multiphase fitting by initially fitting to the mean over repeats",
action="store_true",
default=False)
group.add_option("--mp-biascorr",
help="Use supervoxel-based bias correction",
action="store_true",
default=False)
group.add_option(
"--mp-biascorr-sv",
help="Number of supervoxels to use in bias correction",
type="int",
default=8)
group.add_option(
"--mp-biascorr-comp",
help="Supervoxels compactness to use in bias correction",
type="float",
default=0.1)
group.add_option(
"--mp-biascorr-sigma",
help="Pre-supervoxel smoothing width in bias correction",
type="float",
default=0.5)
group.add_option(
"--mp-biascorr-simple",
help="Use simplified form of supervoxel-based bias correction",
action="store_true",
default=False)
groups.append(group)
return groups