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 native 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