nipype.interfaces.niftyfit.asl module¶
The ASL module of niftyfit, which wraps the fitting methods in NiftyFit.
FitAsl¶
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.
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'
- Mandatory Inputs:
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).- Optional Inputs:
args (a 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) – 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) – In plane PV kernel size [3x3]. Maps to a command-line argument:
-pv2 %d
.pv3 (a 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_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
.- Outputs:
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.