interfaces.niftyfit.asl

FitAsl

Link to code

Wraps command fit_asl

Interface for executable fit_asl from Niftyfit platform.

Use NiftyFit to perform ASL fitting.

ASL fitting routines (following EU Cost Action White Paper recommendations) Fits Cerebral Blood Flow maps in the first instance.

Source code

Examples

>>> from nipype.interfaces import niftyfit
>>> node = niftyfit.FitAsl()
>>> node.inputs.source_file = 'asl.nii.gz'
>>> node.cmdline
'fit_asl -source asl.nii.gz -cbf asl_cbf.nii.gz -error asl_error.nii.gz -syn asl_syn.nii.gz'

Inputs:

[Mandatory]
source_file: (a file name)
        Filename of the 4D ASL (control/label) source image (mandatory).
        flag: -source %s, position: 1

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
cbf_file: (a file name)
        Filename of the Cerebral Blood Flow map (in ml/100g/min).
        flag: -cbf %s
dpld: (a float)
        Difference in labelling delay per slice [0.0 ms/slice.
        flag: -dPLD %f
dt_inv2: (a float)
        Difference in inversion time per slice [0ms/slice].
        flag: -dTinv2 %f
eff: (a float)
        Labelling efficiency [0.99 (pasl), 0.85 (pcasl)], ensure any
        background suppression pulses are included in -eff
        flag: -eff %f
environ: (a dictionary with keys which are a bytes or None or a value
         of class 'str' and with values which are a bytes or None or a value
         of class 'str', nipype default value: {})
        Environment variables
error_file: (a file name)
        Filename of the CBF error map.
        flag: -error %s
gm_plasma: (a float)
        Plasma/GM water partition [0.95ml/g].
        flag: -gmL %f
gm_t1: (a float)
        T1 of GM [1150ms].
        flag: -gmT1 %f
gm_ttt: (a float)
        Time to GM [ATT+0ms].
        flag: -gmTTT %f
ir_output: (a file name)
        Output of [1,2,5]s Inversion Recovery fitting.
        flag: -IRoutput %s
ir_volume: (a file name)
        Filename of a [1,2,5]s Inversion Recovery volume (T1/M0 fitting
        carried out internally).
        flag: -IRvolume %s
ldd: (a float)
        Labelling Duration [1800ms].
        flag: -LDD %f
m0map: (a file name)
        Filename of the estimated input M0 map.
        flag: -m0map %s
m0mape: (a file name)
        Filename of the estimated input M0 map error.
        flag: -m0mape %s
mask: (a file name)
        Filename of image mask.
        flag: -mask %s, position: 2
mul: (a float)
        Multiply CBF by this value (e.g. if CL are mislabelled use -1.0).
        flag: -mul %f
mulgm: (a boolean)
        Multiply CBF by segmentation [Off].
        flag: -sig
out: (a float)
        Outlier rejection for multi CL volumes (enter z-score threshold
        (e.g. 2.5)) [off].
        flag: -out %f
pasl: (a boolean)
        Fit PASL ASL data [default]
        flag: -pasl
pcasl: (a boolean)
        Fit PCASL ASL data
        flag: -pcasl
plasma_coeff: (a float)
        Single plasma/tissue partition coefficient [0.9ml/g].
        flag: -L %f
pld: (a float)
        Post Labelling Delay [2000ms].
        flag: -PLD %f
pv0: (an integer (int or long))
        Simple PV correction (CBF=vg*CBFg + vw*CBFw, with CBFw=f*CBFg)
        [0.25].
        flag: -pv0 %d
pv2: (an integer (int or long))
        In plane PV kernel size [3x3].
        flag: -pv2 %d
pv3: (a tuple of the form: (an integer (int or long), an integer (int
         or long), an integer (int or long)))
        3D kernel size [3x3x1].
        flag: -pv3 %d %d %d
pv_threshold: (a boolean)
        Set PV threshold for switching off LSQR [O.05].
        flag: -pvthreshold
seg: (a file name)
        Filename of the 4D segmentation (in ASL space) for L/T1 estimation
        and PV correction {WM,GM,CSF}.
        flag: -seg %s
segstyle: (a boolean)
        Set CBF as [gm,wm] not [wm,gm].
        flag: -segstyle
sig: (a boolean)
        Use sigmoid to estimate L from T1: L(T1|gmL,wmL) [Off].
        flag: -sig
syn_file: (a file name)
        Filename of the synthetic ASL data.
        flag: -syn %s
t1_art_cmp: (a float)
        T1 of arterial component [1650ms].
        flag: -T1a %f
t1map: (a file name)
        Filename of the estimated input T1 map (in ms).
        flag: -t1map %s
t_inv1: (a float)
        Saturation pulse time [800ms].
        flag: -Tinv1 %f
t_inv2: (a float)
        Inversion time [2000ms].
        flag: -Tinv2 %f
wm_plasma: (a float)
        Plasma/WM water partition [0.82ml/g].
        flag: -wmL %f
wm_t1: (a float)
        T1 of WM [800ms].
        flag: -wmT1 %f
wm_ttt: (a float)
        Time to WM [ATT+0ms].
        flag: -wmTTT %f

Outputs:

cbf_file: (a file name)
        Filename of the Cerebral Blood Flow map (in ml/100g/min).
error_file: (a file name)
        Filename of the CBF error map.
syn_file: (a file name)
        Filename of the synthetic ASL data.