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_file : a 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).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
cbf_file : a 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.
dpld : a float
Difference in labelling delay per slice [0.0 ms/slice. Maps to a command-line argument: -dPLD %f.
dt_inv2 : a float
Difference in inversion time per slice [0ms/slice]. Maps to a command-line argument: -dTinv2 %f.
eff : a 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.
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’
Environment variables. (Nipype default value: {})
error_file : a pathlike object or string representing a file
Filename of the CBF error map. Maps to a command-line argument: -error %s.
gm_plasma : a float
Plasma/GM water partition [0.95ml/g]. Maps to a command-line argument: -gmL %f.
gm_t1 : a float
T1 of GM [1150ms]. Maps to a command-line argument: -gmT1 %f.
gm_ttt : a float
Time to GM [ATT+0ms]. Maps to a command-line argument: -gmTTT %f.
ir_output : a 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_volume : a 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.
ldd : a float
Labelling Duration [1800ms]. Maps to a command-line argument: -LDD %f.
m0map : a pathlike object or string representing an existing file
Filename of the estimated input M0 map. Maps to a command-line argument: -m0map %s.
m0mape : a pathlike object or string representing an existing file
Filename of the estimated input M0 map error. Maps to a command-line argument: -m0mape %s.
mask : a pathlike object or string representing an existing file
Filename of image mask. Maps to a command-line argument: -mask %s (position: 2).
mul : a float
Multiply CBF by this value (e.g. if CL are mislabelled use -1.0). Maps to a command-line argument: -mul %f.
mulgm : a boolean
Multiply CBF by segmentation [Off]. Maps to a command-line argument: -sig.
out : a float
Outlier rejection for multi CL volumes (enter z-score threshold (e.g. 2.5)) [off]. Maps to a command-line argument: -out %f.
pasl : a boolean
Fit PASL ASL data [default]. Maps to a command-line argument: -pasl.
pcasl : a boolean
Fit PCASL ASL data. Maps to a command-line argument: -pcasl.
plasma_coeff : a float
Single plasma/tissue partition coefficient [0.9ml/g]. Maps to a command-line argument: -L %f.
pld : a float
Post Labelling Delay [2000ms]. Maps to a command-line argument: -PLD %f.
pv0 : an integer (int or long)
Simple PV correction (CBF=vg*CBFg + vw*CBFw, with CBFw=f*CBFg) [0.25]. Maps to a command-line argument: -pv0 %d.
pv2 : an integer (int or long)
In plane PV kernel size [3x3]. Maps to a command-line 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]. Maps to a command-line argument: -pv3 %d %d %d.
pv_threshold : a boolean
Set PV threshold for switching off LSQR [O.05]. Maps to a command-line argument: -pvthreshold.
seg : a 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.
segstyle : a boolean
Set CBF as [gm,wm] not [wm,gm]. Maps to a command-line argument: -segstyle.
sig : a boolean
Use sigmoid to estimate L from T1: L(T1|gmL,wmL) [Off]. Maps to a command-line argument: -sig.
syn_file : a pathlike object or string representing a file
Filename of the synthetic ASL data. Maps to a command-line argument: -syn %s.
t1_art_cmp : a float
T1 of arterial component [1650ms]. Maps to a command-line argument: -T1a %f.
t1map : a 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_inv1 : a float
Saturation pulse time [800ms]. Maps to a command-line argument: -Tinv1 %f.
t_inv2 : a float
Inversion time [2000ms]. Maps to a command-line argument: -Tinv2 %f.
wm_plasma : a float
Plasma/WM water partition [0.82ml/g]. Maps to a command-line argument: -wmL %f.
wm_t1 : a float
T1 of WM [800ms]. Maps to a command-line argument: -wmT1 %f.
wm_ttt : a float
Time to WM [ATT+0ms]. Maps to a command-line argument: -wmTTT %f.
cbf_file : a pathlike object or string representing an existing file
Filename of the Cerebral Blood Flow map (in ml/100g/min).
error_file : a pathlike object or string representing an existing file
Filename of the CBF error map.
syn_file : a pathlike object or string representing an existing file
Filename of the synthetic ASL data.