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