3 d@shdZddlmZmZmZmZddlmZddlmZGdddeZ Gdd d eZ Gd d d eZ d S) zX The QT1 module of niftyfit, which wraps the Multi-Echo T1 fitting methods in NiftyFit. ) TraitedSpecFiletraitsCommandLineInputSpec)NiftyFitCommand)get_custom_pathc@sXeZdZdZdZeddedddZedgdd d d Zedgd d dd ZdZedgdded Z edgdddd Z dZedgdded Z edgdddd Z edgdddd Z edddd d!Zed"dd#d$d!Zejd%d&d'd(Zejd)d*d+d(Zd,Zejed-d.d/Zd0Zejejejed1d2d(Zd3Zejed4d5d(Zejd6d7d8d(Zejejejejd9d:d;d(Zejdd(Zejd?d@dAd(ZejdBdCdDd(ZejejdEdFdGdHdIZ eddJdKdLZ!eddMdNdLZ"ejdOdPdQZ#ejdRdSdQZ$ejdTdUdQZ%ejejdVdWdHdXZ&dYZeddZedLZ'd[Zedd\edLZ(edd]d^d_Z)ejd`dadQZ*ejdbdcdQZ+ejdddedQZ,dfS)gFitQt1InputSpeczInput Spec for FitQt1.z.Filename of the 4D Multi-Echo T1 source image.rTz -source %s)positionexistsdescargstr mandatory source_filez%s_t1map.nii.gzz -t1map %sz0Filename of the estimated output T1 map (in ms).)Z name_sourceZ name_templater r z%s_m0map.nii.gzz -m0map %sz'Filename of the estimated input M0 map.z5Filename of the estimated output multi-parameter map.z%s_mcmap.nii.gzz -mcmap %sz%s_comp.nii.gzz-comp %sz1Filename of the estimated multi-component T1 map.z=Filename of the error map (symmetric matrix, [Diag,OffDiag]).z%s_error.nii.gzz -error %sz %s_syn.nii.gzz-syn %sz#Filename of the synthetic ASL data.z %s_res.nii.gzz-res %sz#Filename of the model fit residualsrzFilename of image mask.z-mask %s)r r r r zFilename of parameter prior.z -prior %szTE Echo Time [0ms!].z-TE %f)r r r zTR Repetition Time [10s!].z-TR %fz6Number of components to fit [1] (currently IR/SR only)z-nc %d)r r r z;Set LM parameters (initial value, decrease rate) [100,1.2].z -lm %f %fz1Use Gauss-Newton algorithm [Levenberg-Marquardt].z-gnzFit to single slice number.z -slice %d zFit to single voxel only.z-voxel %d %d %d zNLSQR iterations [100].z -maxit %d z&Saturation Recovery fitting [default].z-SR z%Inversion Recovery fitting [default].z-IR z'Inversion times for T1 data [1s,2s,5s].z-TIs %s )r r r sepz -TIlist %sz$Filename of list of pre-defined TIs.)r r r z -T1list %sz#Filename of list of pre-defined T1sz Minimum tissue T1 value [400ms].z -T1min %f)r r z!Maximum tissue T1 value [4000ms].z -T1max %fzSpoiled Gradient Echo fittingz-SPGRz Flip anglesz -flips %s)r r rz2Filename of list of pre-defined flip angles (deg).z -fliplist %sz:Filename of B1 estimate for fitting (or include in prior).z -b1map %sz(Filename of mc samples (ascii text file)z -mcout %s)r r r z Number of samples to keep [100].z -mcsamples %dz%Number of iterations to run [10,000].z -mcmaxit %dz(Fraction of iterations to accept [0.23].z-acceptance %fN)-__name__ __module__ __qualname____doc__r rr t1map_file m0map_file mcmap_file comp_file error_filesyn_fileres_filemaskZpriorrZFloatZte_valueZtr_valueZIntZnb_compTupleZlm_valZBoolZgn_flagZslice_noZvoxelZmaxitZsr_flagZir_flagListZtisZtis_listZt1_listZt1minZt1maxZspgrZflipsZ flips_listZb1mapZmcoutZ mcsamplesZmcmaxitZ acceptancer,r,@/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/niftyfit/qt1.pyr s         r c@s^eZdZdZeddZeddZdZeedZeddZ dZeedZ eddZ ed dZ d S) FitQt1OutputSpeczOutput Spec for FitQt1.z/Filename of the estimated output T1 map (in ms))r zFilename of the m0 mapz4Filename of the estimated output multi-parameter mapz1Filename of the estimated multi-component T1 map.z`_ Examples -------- >>> from nipype.interfaces.niftyfit import FitQt1 >>> fit_qt1 = FitQt1() >>> fit_qt1.inputs.source_file = 'TI4D.nii.gz' >>> fit_qt1.cmdline 'fit_qt1 -source TI4D.nii.gz -comp TI4D_comp.nii.gz -error TI4D_error.nii.gz -m0map TI4D_m0map.nii.gz -mcmap TI4D_mcmap.nii.gz -res TI4D_res.nii.gz -syn TI4D_syn.nii.gz -t1map TI4D_t1map.nii.gz' Zfit_qt1Z NIFTYFITDIR)Zenv_dirZ_fit_qt1N) rrr r!rZ_cmdr Z input_specr.Z output_spec_suffixr,r,r,r-r/s  r/N) r!baserrrrrZ niftyreg.baserr r.r/r,r,r,r-s