interfaces.niftyfit.asl¶
FitAsl¶
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.
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]
pasl: (a boolean)
Fit PASL ASL data [default]
argument: ``-pasl``
pcasl: (a boolean)
Fit PCASL ASL data
argument: ``-pcasl``
cbf_file: (a file name)
Filename of the Cerebral Blood Flow map (in ml/100g/min).
argument: ``-cbf %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``
t1map: (a file name)
Filename of the estimated input T1 map (in ms).
argument: ``-t1map %s``
m0map: (a file name)
Filename of the estimated input M0 map.
argument: ``-m0map %s``
m0mape: (a file name)
Filename of the estimated input M0 map error.
argument: ``-m0mape %s``
ir_volume: (a file name)
Filename of a [1,2,5]s Inversion Recovery volume (T1/M0 fitting
carried out internally).
argument: ``-IRvolume %s``
ir_output: (a file name)
Output of [1,2,5]s Inversion Recovery fitting.
argument: ``-IRoutput %s``
mask: (a file name)
Filename of image mask.
argument: ``-mask %s``, position: 2
t1_art_cmp: (a float)
T1 of arterial component [1650ms].
argument: ``-T1a %f``
plasma_coeff: (a float)
Single plasma/tissue partition coefficient [0.9ml/g].
argument: ``-L %f``
eff: (a float)
Labelling efficiency [0.99 (pasl), 0.85 (pcasl)], ensure any
background suppression pulses are included in -eff
argument: ``-eff %f``
out: (a float)
Outlier rejection for multi CL volumes (enter z-score threshold
(e.g. 2.5)) [off].
argument: ``-out %f``
pld: (a float)
Post Labelling Delay [2000ms].
argument: ``-PLD %f``
ldd: (a float)
Labelling Duration [1800ms].
argument: ``-LDD %f``
dpld: (a float)
Difference in labelling delay per slice [0.0 ms/slice.
argument: ``-dPLD %f``
t_inv1: (a float)
Saturation pulse time [800ms].
argument: ``-Tinv1 %f``
t_inv2: (a float)
Inversion time [2000ms].
argument: ``-Tinv2 %f``
dt_inv2: (a float)
Difference in inversion time per slice [0ms/slice].
argument: ``-dTinv2 %f``
gm_t1: (a float)
T1 of GM [1150ms].
argument: ``-gmT1 %f``
gm_plasma: (a float)
Plasma/GM water partition [0.95ml/g].
argument: ``-gmL %f``
gm_ttt: (a float)
Time to GM [ATT+0ms].
argument: ``-gmTTT %f``
wm_t1: (a float)
T1 of WM [800ms].
argument: ``-wmT1 %f``
wm_plasma: (a float)
Plasma/WM water partition [0.82ml/g].
argument: ``-wmL %f``
wm_ttt: (a float)
Time to WM [ATT+0ms].
argument: ``-wmTTT %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``
sig: (a boolean)
Use sigmoid to estimate L from T1: L(T1|gmL,wmL) [Off].
argument: ``-sig``
pv0: (an integer (int or long))
Simple PV correction (CBF=vg*CBFg + vw*CBFw, with CBFw=f*CBFg)
[0.25].
argument: ``-pv0 %d``
pv2: (an integer (int or long))
In plane PV kernel size [3x3].
argument: ``-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].
argument: ``-pv3 %d %d %d``
mul: (a float)
Multiply CBF by this value (e.g. if CL are mislabelled use -1.0).
argument: ``-mul %f``
mulgm: (a boolean)
Multiply CBF by segmentation [Off].
argument: ``-sig``
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``
args: (a unicode string)
Additional parameters to the command
argument: ``%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
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.