nipype.interfaces.niftyfit.asl module

The ASL module of niftyfit, which wraps the fitting methods in NiftyFit.

FitAsl

Link to code

Bases: NiftyFitCommand

Wrapped executable: 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'
source_filea pathlike object or string representing an existing file

Filename of the 4D ASL (control/label) source image (mandatory). Maps to a command-line argument: -source %s (position: 1).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

cbf_filea pathlike object or string representing a file

Filename of the Cerebral Blood Flow map (in ml/100g/min). Maps to a command-line argument: -cbf %s.

dplda float

Difference in labelling delay per slice [0.0 ms/slice. Maps to a command-line argument: -dPLD %f.

dt_inv2a float

Difference in inversion time per slice [0ms/slice]. Maps to a command-line argument: -dTinv2 %f.

effa float

Labelling efficiency [0.99 (pasl), 0.85 (pcasl)], ensure any background suppression pulses are included in -eff. Maps to a command-line argument: -eff %f.

environa 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’

Environment variables. (Nipype default value: {})

error_filea pathlike object or string representing a file

Filename of the CBF error map. Maps to a command-line argument: -error %s.

gm_plasmaa float

Plasma/GM water partition [0.95ml/g]. Maps to a command-line argument: -gmL %f.

gm_t1a float

T1 of GM [1150ms]. Maps to a command-line argument: -gmT1 %f.

gm_ttta float

Time to GM [ATT+0ms]. Maps to a command-line argument: -gmTTT %f.

ir_outputa pathlike object or string representing an existing file

Output of [1,2,5]s Inversion Recovery fitting. Maps to a command-line argument: -IRoutput %s.

ir_volumea pathlike object or string representing an existing file

Filename of a [1,2,5]s Inversion Recovery volume (T1/M0 fitting carried out internally). Maps to a command-line argument: -IRvolume %s.

ldda float

Labelling Duration [1800ms]. Maps to a command-line argument: -LDD %f.

m0mapa pathlike object or string representing an existing file

Filename of the estimated input M0 map. Maps to a command-line argument: -m0map %s.

m0mapea pathlike object or string representing an existing file

Filename of the estimated input M0 map error. Maps to a command-line argument: -m0mape %s.

maska pathlike object or string representing an existing file

Filename of image mask. Maps to a command-line argument: -mask %s (position: 2).

mula float

Multiply CBF by this value (e.g. if CL are mislabelled use -1.0). Maps to a command-line argument: -mul %f.

mulgma boolean

Multiply CBF by segmentation [Off]. Maps to a command-line argument: -sig.

outa float

Outlier rejection for multi CL volumes (enter z-score threshold (e.g. 2.5)) [off]. Maps to a command-line argument: -out %f.

pasla boolean

Fit PASL ASL data [default]. Maps to a command-line argument: -pasl.

pcasla boolean

Fit PCASL ASL data. Maps to a command-line argument: -pcasl.

plasma_coeffa float

Single plasma/tissue partition coefficient [0.9ml/g]. Maps to a command-line argument: -L %f.

plda float

Post Labelling Delay [2000ms]. Maps to a command-line argument: -PLD %f.

pv0an integer

Simple PV correction (CBF=vg*CBFg + vw*CBFw, with CBFw=f*CBFg) [0.25]. Maps to a command-line argument: -pv0 %d.

pv2an integer

In plane PV kernel size [3x3]. Maps to a command-line argument: -pv2 %d.

pv3a tuple of the form: (an integer, an integer, an integer)

3D kernel size [3x3x1]. Maps to a command-line argument: -pv3 %d %d %d.

pv_thresholda boolean

Set PV threshold for switching off LSQR [O.05]. Maps to a command-line argument: -pvthreshold.

sega pathlike object or string representing an existing file

Filename of the 4D segmentation (in ASL space) for L/T1 estimation and PV correction {WM,GM,CSF}. Maps to a command-line argument: -seg %s.

segstylea boolean

Set CBF as [gm,wm] not [wm,gm]. Maps to a command-line argument: -segstyle.

siga boolean

Use sigmoid to estimate L from T1: L(T1|gmL,wmL) [Off]. Maps to a command-line argument: -sig.

syn_filea pathlike object or string representing a file

Filename of the synthetic ASL data. Maps to a command-line argument: -syn %s.

t1_art_cmpa float

T1 of arterial component [1650ms]. Maps to a command-line argument: -T1a %f.

t1mapa pathlike object or string representing an existing file

Filename of the estimated input T1 map (in ms). Maps to a command-line argument: -t1map %s.

t_inv1a float

Saturation pulse time [800ms]. Maps to a command-line argument: -Tinv1 %f.

t_inv2a float

Inversion time [2000ms]. Maps to a command-line argument: -Tinv2 %f.

wm_plasmaa float

Plasma/WM water partition [0.82ml/g]. Maps to a command-line argument: -wmL %f.

wm_t1a float

T1 of WM [800ms]. Maps to a command-line argument: -wmT1 %f.

wm_ttta float

Time to WM [ATT+0ms]. Maps to a command-line argument: -wmTTT %f.

cbf_filea pathlike object or string representing an existing file

Filename of the Cerebral Blood Flow map (in ml/100g/min).

error_filea pathlike object or string representing an existing file

Filename of the CBF error map.

syn_filea pathlike object or string representing an existing file

Filename of the synthetic ASL data.