3 dN@sdZddlZddlZddlmZddlmZmZddlm Z m Z m Z m Z m Z mZdd lmZmZmZmZmZd Zejd ZGd d d e ZGddde ZGddde ZGddde ZGddde ZGddde ZGdddeZGdddeZGddde ZGddde Z Gd d!d!eZ!Gd"d#d#e Z"Gd$d%d%e Z#Gd&d'd'eZ$Gd(d)d)e Z%Gd*d+d+e Z&Gd,d-d-eZ'Gd.d/d/e Z(dS)0zLProvides interfaces to various longitudinal commands provided by freesurfer N)logging)split_filenamecopyfile) FSCommand FSTraitedSpecFSScriptCommandFSScriptOutputSpecFSCommandOpenMPFSTraitedSpecOpenMP) isdefined TraitedSpecFiletraits DirectoryZrestructuredtextznipype.interfacec@s>eZdZeddddddZejdddddZedddd Z d S) MPRtoMNI305InputSpecTZTODO)exists mandatory usedefaultdesczinput atlas file)rrrz%sz%the input file prefix for MPRtoMNI305)argstrrrN) __name__ __module__ __qualname__r reference_dirrStringtargetrin_filer!r!K/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/freesurfer/registration.pyrs rc@seZdZedddZdS)MPRtoMNI305OutputSpecFz6The output file '_to__t4_vox2vox.txt')rrN)rrrrout_filer!r!r!r"r#(sr#csTeZdZdZdZeZeZfddZ fddZ ddZ d d Z fd d Z ZS) MPRtoMNI305a  For complete details, see FreeSurfer documentation Examples -------- >>> from nipype.interfaces.freesurfer import MPRtoMNI305, Info >>> mprtomni305 = MPRtoMNI305() >>> mprtomni305.inputs.target = 'structural.nii' >>> mprtomni305.inputs.reference_dir = '.' # doctest: +SKIP >>> mprtomni305.cmdline # doctest: +SKIP 'mpr2mni305 output' >>> mprtomni305.inputs.out_file = 'struct_out' # doctest: +SKIP >>> mprtomni305.cmdline # doctest: +SKIP 'mpr2mni305 struct_out' # doctest: +SKIP >>> mprtomni305.inputs.environ['REFDIR'] == os.path.join(Info.home(), 'average') # doctest: +SKIP True >>> mprtomni305.inputs.environ['MPR2MNI305_TARGET'] # doctest: +SKIP 'structural' >>> mprtomni305.run() # doctest: +SKIP Z mpr2mni305c s6tt|jf||jj|jd|jj|jddS)Nrr)superr%__init__inputsZon_trait_change_environ_update)selfr() __class__r!r"r'IszMPRtoMNI305.__init__csV|dkr dS|dkrBt|\}}}t|tjj||ddd|Stt|j|||S) Nrrrr Tcontent)copyZ hashmethod)rr)rrospathabspathr&r% _format_arg)r*optspecval_retvalext)r+r!r"r1NszMPRtoMNI305._format_argcCs,|jj}|jj}||jjd<||jjd<dS)NZMPR2MNI305_TARGETZREFDIR)r(rrenviron)r*Zrefdirrr!r!r"r)Zs zMPRtoMNI305._environ_updatecCs t|dS)Nr)r)r*fnamer!r!r" _get_fnameaszMPRtoMNI305._get_fnamecsDtt|j}dj|j|jjd|jjddg}tj j ||d<|S)Nr5ZtoZt4z vox2vox.txtr$) r&r% _list_outputsjoinr:r(r rr.r/r0)r*outputsfullname)r+r!r"r;ds zMPRtoMNI305._list_outputs)rrr__doc___cmdr input_specr# output_specr'r1r)r:r; __classcell__r!r!)r+r"r%.s  r%c@sTeZdZeddddddZeddddddZeddddd dZed ddd d d ZdS)RegisterAVItoTalairachInputSpecz%sTrzThe input file)rrrpositionrrzThe target filer zThe vox2vox fileztalairach.auto.xfmrzThe transform output)rrrErN)rrrrr rZvox2voxr$r!r!r!r"rDssrDc@seZdZedddZdS) RegisterAVItoTalairachOutputSpecFz*The output file for RegisterAVItoTalairach)rrN)rrrrr$r!r!r!r"rFsrFc@s$eZdZdZdZeZeZddZ dS)RegisterAVItoTalairachaL converts the vox2vox from talairach_avi to a talairach.xfm file This is a script that converts the vox2vox from talairach_avi to a talairach.xfm file. It is meant to replace the following cmd line: tkregister2_cmdl --mov $InVol --targ $FREESURFER_HOME/average/mni305.cor.mgz --xfmout ${XFM} --vox2vox talsrcimg_to_${target}_t4_vox2vox.txt --noedit --reg talsrcimg.reg.tmp.dat set targ = $FREESURFER_HOME/average/mni305.cor.mgz set subject = mgh-02407836-v2 set InVol = $SUBJECTS_DIR/$subject/mri/orig.mgz set vox2vox = $SUBJECTS_DIR/$subject/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Examples ======== >>> from nipype.interfaces.freesurfer import RegisterAVItoTalairach >>> register = RegisterAVItoTalairach() >>> register.inputs.in_file = 'structural.mgz' # doctest: +SKIP >>> register.inputs.target = 'mni305.cor.mgz' # doctest: +SKIP >>> register.inputs.vox2vox = 'talsrcimg_to_structural_t4_vox2vox.txt' # doctest: +SKIP >>> register.cmdline # doctest: +SKIP 'avi2talxfm structural.mgz mni305.cor.mgz talsrcimg_to_structural_t4_vox2vox.txt talairach.auto.xfm' >>> register.run() # doctest: +SKIP Z avi2talxfmcCs$|jj}tjj|jj|d<|S)Nr$)rBgetr.r/r0r(r$)r*r=r!r!r"r;s z$RegisterAVItoTalairach._list_outputsN) rrrr?r@rDrArFrBr;r!r!r!r"rGs rGc @seZdZeddddddZeddddddZeddd gd dddd d ZejdddZ eddddZ ej dddZ eddddZ dS)EMRegisterInputSpecz%sTrzin brain volume)rrrrErr z template gcaFr z%s_transform.ltarzoutput transform)rr name_source name_template hash_fileskeep_extensionrErz-skullz'align to atlas containing skull (uns=5))rrz-mask %szuse volume as a mask)rrrz-uns %dzHalign to atlas containing skull setting unknown_nbr_spacing = nbrspacingz-t %szPreviously computed transformN)rrrrr templater$rBoolZskullmaskIntZ nbrspacingZ transformr!r!r!r"rIs&rIc@seZdZedddZdS)EMRegisterOutputSpecFzoutput transform)rrN)rrrrr$r!r!r!r"rUsrUc@s$eZdZdZdZeZeZddZ dS) EMRegisteraThis program creates a tranform in lta format Examples ======== >>> from nipype.interfaces.freesurfer import EMRegister >>> register = EMRegister() >>> register.inputs.in_file = 'norm.mgz' >>> register.inputs.template = 'aseg.mgz' >>> register.inputs.out_file = 'norm_transform.lta' >>> register.inputs.skull = True >>> register.inputs.nbrspacing = 9 >>> register.cmdline 'mri_em_register -uns 9 -skull norm.mgz aseg.mgz norm_transform.lta' Zmri_em_registercCs$|jj}tjj|jj|d<|S)Nr$)rBrHr.r/r0r(r$)r*r=r!r!r"r;s zEMRegister._list_outputsN) rrrr?r@rIrArUrBr;r!r!r!r"rVs rVc@steZdZedddddddZedddddd Zedddd d Zedd ddddZej ddgddZ eddddZ dS)RegisterInputSpecz%sTrz(Surface to register, often {hemi}.sphere)rrrrErrr z4The data to register to. In normal recon-all usage, z,this is a template file for average surface.)rrrrErzIUndocumented mandatory input file ${SUBJECTS_DIR}/surf/{hemisphere}.sulc )rrrrFrz+Output surface file to capture registration)rrrEZgenfilerz-curv in_smoothwmz*Use smoothwm curvature for final alignment)rrequiresrzCUndocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm )rrrNrNrOz`The data to register to. In normal recon-all usage, this is a template file for average surface.rP) rrrrin_surfrZin_sulcr$rrRcurvrXr!r!r!r"rWsBrWc@seZdZedddZdS)RegisterOutputSpecFz+Output surface file to capture registration)rrN)rrrrr$r!r!r!r"r\sr\cs<eZdZdZdZeZeZfddZ ddZ ddZ Z S) RegisteraThis program registers a surface to an average surface template. Examples ======== >>> from nipype.interfaces.freesurfer import Register >>> register = Register() >>> register.inputs.in_surf = 'lh.pial' >>> register.inputs.in_smoothwm = 'lh.pial' >>> register.inputs.in_sulc = 'lh.pial' >>> register.inputs.target = 'aseg.mgz' >>> register.inputs.out_file = 'lh.pial.reg' >>> register.inputs.curv = True >>> register.cmdline 'mris_register -curv lh.pial aseg.mgz lh.pial.reg' Z mris_registercs"|dkr|jStt|j|||S)Nr[)rr&r]r1)r*r2r3r4)r+r!r"r14szRegister._format_argcCs|dkr|j|SdS)Nr$)r;)r*namer!r!r" _gen_filename9s zRegister._gen_filenamecCsJ|jj}t|jjr.tjj|jj|d<ntjj|jjd|d<|S)Nr$z.reg) rBrHrr(r$r.r/r0rZ)r*r=r!r!r"r;>s   zRegister._list_outputs) rrrr?r@rWrAr\rBr1r_r;rCr!r!)r+r"r]s r]c @sdeZdZeddddddZeddddddZejd d Zejd d d Z eddddddgdddZ dS)PaintInputSpecz%sTr z1Surface file with grid (vertices) onto which the z+template data is to be sampled or 'painted')rrrrErrz Template filez"Frame number of the input template)rz-a %dzAverage curvature patterns)rrFrz %s.avg_curvrZz6File containing a surface-worth of per-vertex values, zsaved in 'curvature' format.)rrrErKrLrJrMrNrOz\Surface file with grid (vertices) onto which the template data is to be sampled or 'painted'rNrPzRFile containing a surface-worth of per-vertex values, saved in 'curvature' format.) rrrrrZrQrrTtemplate_paramZaveragesr$r!r!r!r"r`Gs* r`c@seZdZedddZdS)PaintOutputSpecFzRFile containing a surface-worth of per-vertex values, saved in 'curvature' format.)rrN)rrrrr$r!r!r!r"rbdsrbcs4eZdZdZdZeZeZfddZ ddZ Z S)Painta This program is useful for extracting one of the arrays ("a variable") from a surface-registration template file. The output is a file containing a surface-worth of per-vertex values, saved in "curvature" format. Because the template data is sampled to a particular surface mesh, this conjures the idea of "painting to a surface". Examples ======== >>> from nipype.interfaces.freesurfer import Paint >>> paint = Paint() >>> paint.inputs.in_surf = 'lh.pial' >>> paint.inputs.template = 'aseg.mgz' >>> paint.inputs.averages = 5 >>> paint.inputs.out_file = 'lh.avg_curv' >>> paint.cmdline 'mrisp_paint -a 5 aseg.mgz lh.pial lh.avg_curv' Z mrisp_paintcsB|dkr.t|jjr.|j|dt|jjStt|j|||S)NrQ#)rr(rarstrr&rcr1)r*r2r3r4)r+r!r"r1s zPaint._format_argcCs$|jj}tjj|jj|d<|S)Nr$)rBrHr.r/r0r(r$)r*r=r!r!r"r;s zPaint._list_outputs) rrrr?r@r`rArbrBr1r;rCr!r!)r+r"rcks  rcc@s"eZdZedddddZedddddgd Zejded ddd d Zejded ddZ ejdedddZ e ddddZ ej ddddgdgddZejddddddZejdej d d!d"d#Zej d$d%dZejd&d'dZejd(d)dZejd*d+dZejd,dd!d-d.Zejejejejd/d0dZejejejejd1d2dZejejejejd3d4dZejejejejd5d6dZejd7d8dZ ej!dd9d:d;Z"ejdd?Z$ej!d@dAdBdCdDZ%ejdEdFdZ&ejdGdHdZ'ejdIdJgdKdLZ(ejdMdJgdNdLZ)ejdOdPdZ*ejdQdRdZ+ejdSdTdZ,dUS)VMRICoregInputSpecz--mov %szsource file to be registeredTF)rrrrz--ref %szreference (target) file subject_id)rrrrxorz--lta %sz%output registration file (LTA format))rdefaultrrz --regdat %sz%output registration file (REG format))rrz --params %szoutput parameters filez--sd %szFreeSurfer SUBJECTS_DIR)rrrz--s %srreference_file subjects_dirz_freesurfer subject ID (implies ``reference_mask == aparc+aseg.mgz`` unless otherwise specified))rrErrhrYr z--dof %dz&number of transform degrees of freedomz --ref-mask %sr z;mask reference volume with given mask, or None if ``False``)rrErz --mov-maskz mask source file with given maskz --threads %dznumber of OpenMP threadsz--no-coord-ditherzturn off coordinate ditheringz--no-intensity-ditherzturn off intensity ditheringz --sep %s...z.set spatial scales, in voxels (default [2, 4]))rZminlenmaxlenrz--trans %g %g %gz,initial translation in mm (implies no_cras0)z--rot %g %g %gzinitial rotation in degreesz--scale %g %g %gz initial scalez--shear %g %g %gzinitial shear (Hxy, Hxz, Hyz)z --no-cras0zPdo not set translation parameters to align centers of source and reference filesz--nitersmax %dzmaximum iterations (default: 4))lowrrz --ftol %ez'floating-point tolerance (default=1e-7)z--linmintol %e)rggY@z--sat %gz$saturation threshold (default=9.999))rphighrrz --conf-refz#conform reference without rescalingz--no-bfzdo not brute force searchz --bf-lim %gno_brute_forcez'constrain brute force search to +/- lim)rrhrz --bf-nsamp %dz'number of samples in brute force searchz --no-smoothz9do not apply smoothing to either reference or source filez --ref-fwhmz!apply smoothing to reference filez --mov-oobz/count source voxels that are out-of-bounds as 0N)-rrrrZ source_filerjrZEither out_lta_file out_reg_fileout_params_filerrkStrrgEnumZdofreference_maskZ source_maskrTZ num_threadsrRZno_coord_ditheringZno_intensity_ditheringListsepTupleZFloatZinitial_translationZinitial_rotationZ initial_scaleZ initial_shearZno_cras0ZRangeZ max_itersZftolZ linmintolZsaturation_thresholdZconform_referencerrZbrute_force_limitZbrute_force_samplesZ no_smoothZref_fwhmZ source_oobr!r!r!r"rfs          rfc@s0eZdZedddZedddZedddZdS)MRICoregOutputSpecTzoutput registration file)rrz"output LTA-style registration filezoutput parameters fileN)rrrrrtrsrur!r!r!r"r|s  r|cs4eZdZdZdZeZeZfddZ ddZ Z S)MRICoregaFThis program registers one volume to another mri_coreg is a C reimplementation of spm_coreg in FreeSurfer Examples ======== >>> from nipype.interfaces.freesurfer import MRICoreg >>> coreg = MRICoreg() >>> coreg.inputs.source_file = 'moving1.nii' >>> coreg.inputs.reference_file = 'fixed1.nii' >>> coreg.inputs.subjects_dir = '.' >>> coreg.cmdline # doctest: +ELLIPSIS 'mri_coreg --lta .../registration.lta --ref fixed1.nii --mov moving1.nii --sd .' If passing a subject ID, the reference mask may be disabled: >>> coreg = MRICoreg() >>> coreg.inputs.source_file = 'moving1.nii' >>> coreg.inputs.subjects_dir = '.' >>> coreg.inputs.subject_id = 'fsaverage' >>> coreg.inputs.reference_mask = False >>> coreg.cmdline # doctest: +ELLIPSIS 'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --mov moving1.nii --sd .' Spatial scales may be specified as a list of one or two separations: >>> coreg.inputs.sep = [4] >>> coreg.cmdline # doctest: +ELLIPSIS 'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --mov moving1.nii --sd .' >>> coreg.inputs.sep = [4, 5] >>> coreg.cmdline # doctest: +ELLIPSIS 'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --sep 5 --mov moving1.nii --sd .' Z mri_coregcsF|dkr|dkr|j|}n|dkr2|dkr2dStt|j|||S) NrtrsruTrxFz --no-ref-mask)rtrsru)r;r&r}r1)r*r2r3r4)r+r!r"r1Is zMRICoreg._format_argcCs|jj}|jj}t|r8|dkr(d}tjj||d<|jj}t|rd|dkrTd}tjj||d<|jj }t|r|dkrd}tjj||d<|S)NTzregistration.ltarszregistration.datrtzregistration.parru) rBrHr(rsrr.r/r0rtru)r*r=rsrtrur!r!r"r;Ps" zMRICoreg._list_outputs) rrrr?r@rfrAr|rBr1r;rCr!r!)r+r"r}!s " r}))r?r.os.pathrrZutils.filemaniprrbaserrr r r r rrrrrZ __docformat__ getLoggerZifloggerrr#r%rDrFrGrIrUrVrWr\r]r`rbrcrfr|r}r!r!r!r"s6    E+,($