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'
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.