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

Outputs:

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