OXASL command reference

The main OXASL command has many options, however most have sensible defaults so in practice only a few typically need to be used. For example usages see the Walkthrough section.

Full option list

Input ASL image:

-i ASLDATA, --asldata=ASLDATA
	ASL data file
--iaf=IAF	input ASl format: diff=differenced,tc=tag-control,ct =control-tag,mp=multiphase,ve=vessel-encoded
--order=ORDER	Data order as sequence of 2 or 3 characters: t=TIs/PLDs, r=repeats, l=labelling (tag/control/phases etc). First character is fastest varying
--tis=TIS	TIs (s) as comma-separated list
--plds=PLDS	PLDs (s) as comma-separated list - alternative to –tis
--ntis=NTIS	Number of TIs (for use when processing does not require actual values)
--nplds=NPLDS	Equivalent to –ntis
--rpts=RPTS	Variable repeats as comma-separated list, one per TI/PLD
--nphases=NPHASES
	For –iaf=mp, number of phases (assumed to be evenly spaced)
--nenc=NENC	For –iaf=ve, number of encoding cycles
--casl	Acquisition was pseudo cASL (pcASL) rather than pASL
--tau=TAU, --taus=TAU, --bolus=TAU
	Bolus duration (s). Can be single value or comma separated list, one per TI/PLD
--slicedt=SLICEDT
	Timing difference between slices (s) for 2D readout
--sliceband=SLICEBAND
	Number of slices per pand in multi-band setup
--artsupp	Arterial suppression (vascular crushing) was used
--ibf=IBF	input block format - alternative to –order for compatibility. rpt=Blocks of repeats (i.e. repeats are slowest varying), tis=Blocsk of TIs/PLDs

Structural image:

-s STRUC, --struc=STRUC
	Structural image
--struc-brain=STRUC_BRAIN, --sbet=STRUC_BRAIN, --struc-bet=STRUC_BRAIN
	Structural image (brain extracted)
--struc2asl=STRUC2ASL
	Structural->ASL transformation matrix
--asl2struc=ASL2STRUC
	ASL->Structural transformation matrix
--wm-seg=WM_SEG
	White matter segmentation of structural image
--gm-seg=GM_SEG
	Grey matter segmentation of structural image
--csf-seg=CSF_SEG
	CSF segmentation of structural image
--fslanat=FSLANAT
	FSL_ANAT output directory for structural information
--fastsrc=FASTSRC
	Images from a FAST segmentation - if not set FAST will be run on structural image
--struc2std=STRUC2STD
	Structural to MNI152 linear registration (.mat)
--struc2std-warp=STRUC2STD_WARP
	Structural to MNI152 non-linear registration (warp)

Main Options:

--wp	Analysis which conforms to the ‘white papers’ (Alsop et al 2014)
--mc	Motion correct data
--fixbat	Fix bolus arrival time
--fixbolus	Fix bolus duration
--artoff	Do not infer arterial component
--spatial-off	Do not include adaptive spatial smoothing on CBF

Acquisition/Data specific:

--bat=BAT	Estimated bolus arrival time (s) - default=0.7 (pASL), 1.3 (cASL)
--batsd=BATSD	Bolus arrival time standard deviation (s)
--t1=T1	Tissue T1 (s)
--t1b=T1B	Blood T1 (s)

Output options:

--save-corrected
	Save corrected input data
--save-reg	Save registration information (transforms etc)
--save-basil	Save Basil modelling output
--save-calib	Save calibration output
--save-all	Save all output (enabled when –debug specified)
--output-stddev, --output-std
	Output standard deviation of estimated variables
--output-var, --vars
	Output variance of estimated variables
--no-report	Don’t try to generate an HTML report

Calibration:

-c CALIB, --calib=CALIB
	Calibration image
--calib-method=CALIB_METHOD, --cmethod=CALIB_METHOD
	Calibration method: voxelwise or refregion
--calib-alpha=CALIB_ALPHA, --alpha=CALIB_ALPHA
	Inversion efficiency
--calib-gain=CALIB_GAIN, --cgain=CALIB_GAIN
	Relative gain between calibration and ASL data
--tr=TR	TR used in calibration sequence (s)

Voxelwise calibration:

--pct=PCT	Tissue/arterial partition coefficiant
--t1t=T1T	T1 of tissue (s)

Reference region calibration:

--mode=MODE	Calibration mode (longtr or satrevoc)
--tissref=TISSREF
	Tissue reference type (csf, wm, gm or none)
--te=TE	Sequence TE (ms)
--t1r=T1R	T1 of reference tissue (s) - defaults: csf 4.3, gm 1.3, wm 1.0
--t2r=T2R	T2/T2* of reference tissue (ms) - defaults T2/T2*: csf 750/400, gm 100/60, wm 50/50
--t2b=T2B	T2/T2* of blood (ms) - default T2/T2*: 150/50)
--refmask=REFMASK
	Reference tissue mask in perfusion/calibration image space
--t2star	Correct with T2* rather than T2 (alters the default T2 values)
--pcr=PCR	Reference tissue partition coefficiant (defaults csf 1.15, gm 0.98, wm 0.82)

longtr mode (calibration image is a control image with a long TR):

satrecov mode (calibration image is a sequnce of control images at various TIs):

--fa=FA	Flip angle (in degrees) for Look-Locker readouts
--lfa=LFA	Lower flip angle (in degrees) for dual FA calibration
--calib-nphases=CALIB_NPHASES
	Number of phases (repetitions) of higher FA
--fixa	Fix the saturation efficiency to 100% (useful if you have a low number of samples)

Registration:

--regfrom=REGFROM
	Registration image (e.g. perfusion weighted image)

Distortion correction using fieldmap:

--fmap=FMAP	fieldmap image (in rad/s)
--fmapmag=FMAPMAG
	fieldmap magnitude image - wholehead extracted
--fmapmagbrain=FMAPMAGBRAIN
	fieldmap magnitude image - brain extracted
--nofmapreg	Do not perform registration of fmap to T1 (use if fmap already in T1-space)

Distortion correction using phase-encode-reversed calibration image (TOPUP):

--cblip=CBLIP

phase-encode-reversed (blipped) calibration image

General distortion correction options:

--echospacing=ECHOSPACING
	Effective EPI echo spacing (sometimes called dwell time) - in seconds
--pedir=PEDIR	Phase encoding direction, dir = x/y/z/-x/-y/-z
--gdcwarp=GDCWARP
	Additional warp image for gradient distortion correction - will be combined with fieldmap or TOPUP distortion correction

Sensitivity correction:

--cref=CREF	Reference image for sensitivity correction
--cact=CACT	Image from coil used for actual ASL acquisition (default: calibration image - only in longtr mode)
--isen=ISEN	User-supplied sensitivity correction in ASL space
--senscorr-auto, --senscorr
	Apply automatic sensitivity correction using bias field from FAST
--senscorr-off	Do not apply any sensitivity correction

Partial volume correction: –pvcorr Apply partial volume correction

Generic:

-o OUTPUT, --output=OUTPUT
	Output directory
--overwrite	Overwrite output directory if it already exists
-m MASK, --mask=MASK
	Brain mask image in ASL space
--optfile=OPTFILE
	File containing additional options
--debug	Debug mode
--version	show program’s version number and exit
-h, --help	show help message and exit