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.
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 |