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# 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 unicode 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 (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`.

> pv2an integer (int or long)

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

> pv3a 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_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.