interfaces.niftyfit.asl

FitAsl

Link to code

Wraps the executable 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).
        argument: ``-source %s``, position: 1

[Optional]
eff: (a float)
        Labelling efficiency [0.99 (pasl), 0.85 (pcasl)], ensure any
        background suppression pulses are included in -eff
        argument: ``-eff %f``
mulgm: (a boolean)
        Multiply CBF by segmentation [Off].
        argument: ``-sig``
ir_volume: (a file name)
        Filename of a [1,2,5]s Inversion Recovery volume (T1/M0 fitting
        carried out internally).
        argument: ``-IRvolume %s``
mul: (a float)
        Multiply CBF by this value (e.g. if CL are mislabelled use -1.0).
        argument: ``-mul %f``
mask: (a file name)
        Filename of image mask.
        argument: ``-mask %s``, position: 2
gm_plasma: (a float)
        Plasma/GM water partition [0.95ml/g].
        argument: ``-gmL %f``
out: (a float)
        Outlier rejection for multi CL volumes (enter z-score threshold
        (e.g. 2.5)) [off].
        argument: ``-out %f``
m0mape: (a file name)
        Filename of the estimated input M0 map error.
        argument: ``-m0mape %s``
t_inv1: (a float)
        Saturation pulse time [800ms].
        argument: ``-Tinv1 %f``
gm_ttt: (a float)
        Time to GM [ATT+0ms].
        argument: ``-gmTTT %f``
pasl: (a boolean)
        Fit PASL ASL data [default]
        argument: ``-pasl``
dpld: (a float)
        Difference in labelling delay per slice [0.0 ms/slice.
        argument: ``-dPLD %f``
ldd: (a float)
        Labelling Duration [1800ms].
        argument: ``-LDD %f``
t_inv2: (a float)
        Inversion time [2000ms].
        argument: ``-Tinv2 %f``
cbf_file: (a file name)
        Filename of the Cerebral Blood Flow map (in ml/100g/min).
        argument: ``-cbf %s``
dt_inv2: (a float)
        Difference in inversion time per slice [0ms/slice].
        argument: ``-dTinv2 %f``
pv0: (an integer (int or long))
        Simple PV correction (CBF=vg*CBFg + vw*CBFw, with CBFw=f*CBFg)
        [0.25].
        argument: ``-pv0 %d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
ir_output: (a file name)
        Output of [1,2,5]s Inversion Recovery fitting.
        argument: ``-IRoutput %s``
m0map: (a file name)
        Filename of the estimated input M0 map.
        argument: ``-m0map %s``
syn_file: (a file name)
        Filename of the synthetic ASL data.
        argument: ``-syn %s``
sig: (a boolean)
        Use sigmoid to estimate L from T1: L(T1|gmL,wmL) [Off].
        argument: ``-sig``
gm_t1: (a float)
        T1 of GM [1150ms].
        argument: ``-gmT1 %f``
pv_threshold: (a boolean)
        Set PV threshold for switching off LSQR [O.05].
        argument: ``-pvthreshold``
segstyle: (a boolean)
        Set CBF as [gm,wm] not [wm,gm].
        argument: ``-segstyle``
wm_ttt: (a float)
        Time to WM [ATT+0ms].
        argument: ``-wmTTT %f``
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].
        argument: ``-pv3 %d %d %d``
error_file: (a file name)
        Filename of the CBF error map.
        argument: ``-error %s``
t1map: (a file name)
        Filename of the estimated input T1 map (in ms).
        argument: ``-t1map %s``
pv2: (an integer (int or long))
        In plane PV kernel size [3x3].
        argument: ``-pv2 %d``
pld: (a float)
        Post Labelling Delay [2000ms].
        argument: ``-PLD %f``
wm_plasma: (a float)
        Plasma/WM water partition [0.82ml/g].
        argument: ``-wmL %f``
wm_t1: (a float)
        T1 of WM [800ms].
        argument: ``-wmT1 %f``
plasma_coeff: (a float)
        Single plasma/tissue partition coefficient [0.9ml/g].
        argument: ``-L %f``
seg: (a file name)
        Filename of the 4D segmentation (in ASL space) for L/T1 estimation
        and PV correction {WM,GM,CSF}.
        argument: ``-seg %s``
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
t1_art_cmp: (a float)
        T1 of arterial component [1650ms].
        argument: ``-T1a %f``
pcasl: (a boolean)
        Fit PCASL ASL data
        argument: ``-pcasl``

Outputs:

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