.. _CLref: 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