3 d(H@sdZddlmZmZmZmZmZddlmZddlm Z GdddeZ Gdd d eZ Gd d d eZ Gd d d eZ GdddeZGdddeZdS)zJ The dwi module of niftyfit, which wraps the fitting methods in NiftyFit. )File TraitedSpectraits isdefinedCommandLineInputSpec)NiftyFitCommand)get_custom_pathc @seZdZdZeddddddZdZeddd dedZd Zed dd dedZedd ddgdZ edd ddgdZ eddddZ dZeddedZ dZe jeddZedgddddZedgd d!d"dZedgd#d$d%dZedgd&d'd(dZedgd)d*d+d,gd-Zedgd.d/d0dZedgd1d2d3dZedgd4d5d6dZedgd7d8d9d:gd-Zd;Ze jdZedgd?d@dAd:gd-ZedgdBdCdDd:gd-ZdEZe jedFdGdHd:dIdJdKd,gdLZe jdMdNdGdOd:dIdJdKd,gdLZdPZe jedQdGdOdHdIdJdKd,gdLZ e jdRdSdGdOdHd:dJdKd,gdLZ!dTZe jedUdGdOdHd:dIdKd,gdLZ"e jdVdWdGdOdHd:dIdJd,gdLZ#e jdXdYdGdOdHd:dIdJdKgdLZ$dZZe jed[d\gd]Z%d^Ze j&e j'e j'd_d\ged`Z(daZe jedbdcgddZ)deZe jedfdZ*eddgdhdZ+e jedid\gddZ,djZe j'edkdZ-e jdldmdZ.e j&e je je jdndodZ/e j'dpdqdZ0e j'drdsdZ1e j'dtdudZ2e j'dvdwdZ3dxZe j'edydZ4edgdzd{d|dZ5e jd}d~dZ6e jdddZ7e j'dddZ8dS)FitDwiInputSpeczInput Spec for FitDwi.rTz -source %sz)The source image containing the dwi data.)positionexistsargstr mandatorydescz2The file containing the bvalues of the source DWI.rz-bval %sz3The file containing the bvectors of the source DWI.z-bvec %sz-TE %szFilename of TEs (ms).te_file)r r rxorzValue of TEs (ms).zThe image maskz-mask %s)r rr z0Filename of parameter priors for -ball and -nod.z -prior %s)r r rz{Rotate the output tensors according to the q/s form of the image (resulting tensors will be in mm coordinates, default: 0).z -rotsform %d)rr source_filez%s_error.nii.gzz!Filename of parameter error maps.z -error %s) name_source name_templaterr z%s_resmap.nii.gzzFilename of model residual map.z-res %sz %s_syn.nii.gzzFilename of synthetic image.z-syn %sz%s_no_diff.nii.gzz'Filename of average no diffusion image.z -nodiff %sz%s_mcmap.nii.gzzDFilename of multi-compartment model parameter map (-ivim,-ball,-nod)z -mcmap %s nodv_flag)rrrr requiresz%s_mdmap.nii.gzzFilename of MD map/ADCz -mdmap %sz%s_famap.nii.gzzFilename of FA mapz -famap %sz%s_v1map.nii.gzzFilename of PDD map [x,y,z]z -v1map %sz%s_rgbmap.nii.gzzFilename of colour-coded FA mapz -rgbmap %sdti_flagzFUse lower triangular (tenmap2) or diagonal, off-diagonal tensor formatz lower-triz diag-off-diag)rZ usedefaultz%s_tenmap.nii.gzz&Filename of tensor map [diag,offdiag].z -tenmap %sz%s_tenmap2.nii.gzz"Filename of tensor map [lower tri]z -tenmap2 %szJFit single exponential to non-directional data [default with no b-vectors]z-mono ivim_flag ball_flag ballv_flagnod_flag)rr r rz'Fit IVIM model to non-directional data.z-ivim mono_flagz.Fit the tensor model [default with b-vectors].z-dtizFit the ball and stick model.z-ballz0Fit the ball and stick model with optimised PDD.z-ballvzFit the NODDI modelz-nodz&Fit the NODDI model with optimised PDDz-nodvz`_ Examples -------- >>> from nipype.interfaces import niftyfit >>> fit_dwi = niftyfit.FitDwi(dti_flag=True) >>> fit_dwi.inputs.source_file = 'dwi.nii.gz' >>> fit_dwi.inputs.bvec_file = 'bvecs' >>> fit_dwi.inputs.bval_file = 'bvals' >>> fit_dwi.inputs.rgbmap_file = 'rgb.nii.gz' >>> fit_dwi.cmdline 'fit_dwi -source dwi.nii.gz -bval bvals -bvec bvecs -dti -error dwi_error.nii.gz -famap dwi_famap.nii.gz -mcout dwi_mcout.txt -mdmap dwi_mdmap.nii.gz -nodiff dwi_no_diff.nii.gz -res dwi_resmap.nii.gz -rgbmap rgb.nii.gz -syn dwi_syn.nii.gz -tenmap2 dwi_tenmap2.nii.gz -v1map dwi_v1map.nii.gz' Zfit_dwi NIFTYFITDIR)env_dirZ_fit_dwicsD|dkr|jjdkrdS|dkr0|jjdkr0dStt|j|||S)Nr3z diag-off-diagr4z lower-tri)inputsr2superr> _format_arg)selfname trait_specvalue) __class__r;r<rDPs zFitDwi._format_arg) r!r"r#r$r _cmdr input_specr= output_spec_suffixrD __classcell__r;r;)rIr<r>/s  r>c @s$eZdZdZdZeddedddZdZedded ddZd Zed ded d Zeddddd Z eddddd Z dZedgdeddZ dZedgdedddgdZ edgdd d!dZ edgd"d#d$dZedgd%d&d'dZedgd(d)d*dZedgd+d,d-dZd.Zejed/d0d1d2d3d4d5d6d7gd8Zd9Zejed/d:d;d2d3d4d5d6d7gd8Zejdd/d?d;d1d2d4d5d6d7gd8Zejd@d/dAd;d1d2d3d5d6d7gd8ZdBZejed/dCd;d1d2d3d4d6d7gd8ZejdDd/dEd;d1d2d3d4d5d7gd8ZejdFd/dGd;d1d2d3d4d5d6gd8ZejdHdIdJZejdKdLdJZdMS)NDwiToolInputSpeczInput Spec for DwiTool.z-The source image containing the fitted model.rTz -source %s)r r rr rz2The file containing the bvalues of the source DWI.rz-bval %sz3The file containing the bvectors of the source DWI.rz-bvec %s)r r rr rz,The B0 image corresponding to the source DWIz-b0 %szThe image maskz-mask %szDFilename of multi-compartment model parameter map (-ivim,-ball,-nod)rz%s_mcmap.nii.gzz -mcmap %s)rrrr z9Filename of synthetic image. Requires: bvec_file/b0_file.z %s_syn.nii.gzz-syn %sr&b0_file)rrrr rz%s_mdmap.nii.gzzFilename of MD map/ADCz -mdmap %sz%s_famap.nii.gzzFilename of FA mapz -famap %sz%s_v1map.nii.gzzFilename of PDD map [x,y,z]z -v1map %sz%s_rgbmap.nii.gzzFilename of colour FA map.z -rgbmap %sz%s_logdti2.nii.gzzFilename of output logdti map.z -logdti2 %szQInput is a single exponential to non-directional data [default with no b-vectors]z-monorr dti_flag2rrrr)rr r rz0Inputs is an IVIM model to non-directional data.z-ivimrz&Input is a tensor model diag/off-diag.z-dtiz(Input is a tensor model lower triangularz-dti2z Input is a ball and stick model.z-ballz3Input is a ball and stick model with optimised PDD.z-ballvzInput is a NODDI modelz-nodz)Input is a NODDI model with optimised PDDz-nodvz%Isotropic diffusivity for -nod [3e-3]z-diso %f)rr z'Parallel diffusivity for -nod [1.7e-3].z-dpr %fN)r!r"r#r$rrrr%r&rQr'r,r*r-r.r/r0 logdti_filerr5rrrrSrrrrr7r8r9r;r;r;r<rOXs(          rOc@sZeZdZdZdZeedZeddZeddZeddZ eddZ eddZ ed dZ d S) DwiToolOutputSpeczOutput Spec for DwiTool.zDFilename of multi-compartment model parameter map (-ivim,-ball,-nod))rzFilename of synthetic imagezFilename of MD map/ADCzFilename of FA mapzFilename of PDD map [x,y,z]zFilename of colour FA mapzFilename of output logdti mapN) r!r"r#r$rrr,r*r-r.r/r0rTr;r;r;r<rUs      rUcs8eZdZdZedddZeZeZ dZ fddZ Z S)DwiToolaInterface for executable dwi_tool from Niftyfit platform. Use DwiTool. Diffusion-Weighted MR Prediction. Predicts DWI from previously fitted models and calculates model derived maps. `Source code `_ Examples -------- >>> from nipype.interfaces import niftyfit >>> dwi_tool = niftyfit.DwiTool(dti_flag=True) >>> dwi_tool.inputs.source_file = 'dwi.nii.gz' >>> dwi_tool.inputs.bvec_file = 'bvecs' >>> dwi_tool.inputs.bval_file = 'bvals' >>> dwi_tool.inputs.mask_file = 'mask.nii.gz' >>> dwi_tool.inputs.b0_file = 'b0.nii.gz' >>> dwi_tool.inputs.rgbmap_file = 'rgb_map.nii.gz' >>> dwi_tool.cmdline 'dwi_tool -source dwi.nii.gz -bval bvals -bvec bvecs -b0 b0.nii.gz -mask mask.nii.gz -dti -famap dwi_famap.nii.gz -logdti2 dwi_logdti2.nii.gz -mcmap dwi_mcmap.nii.gz -mdmap dwi_mdmap.nii.gz -rgbmap rgb_map.nii.gz -syn dwi_syn.nii.gz -v1map dwi_v1map.nii.gz' Zdwi_toolr?)r@Z _dwi_toolcsd|dkr(t|jj s$t|jj r(dS|dkrPt|jj rPt|jj rPdStt|j|||S)Nr*rArTr0)rTr0) rrBr&rQrrSrCrVrD)rErFrGrH)rIr;r<rDPs  zDwiTool._format_arg) r!r"r#r$r rJrOrKrUrLrMrDrNr;r;)rIr<rV-s  rVN)r$baserrrrrrZ niftyreg.baser r r=r>rOrUrVr;r;r;r<s  )G