3 d@sdZddlZddlZddlZddlmZddlmZmZddl m Z m Z m Z m Z mZmZmZmZdd l mZmZmZmZmZmZmZd Zed d d dddddddddddddZd d d ddddddddddddd dd!gZdgZejd"Zdd#d$Z d%d&Z!Gd'd(d(eZ"Gd)d*d*e Z#Gd+d,d,eZ$Gd-d.d.eZ%Gd/d0d0e Z&Gd1d2d2eZ'Gd3d4d4eZ(Gd5d6d6e Z)Gd7d8d8eZ*Gd9d:d:eZ+Gd;d<dd>eZ-Gd?d@d@eZ.GdAdBdBe Z/GdCdDdDeZ0GdEdFdFeZ1GdGdHdHe Z2GdIdJdJeZ3GdKdLdLeZ4GdMdNdNe Z5GdOdPdPeZ6GdQdRdReZ7GdSdTdTe Z8GdUdVdVeZ9GdWdXdXeZ:GdYdZdZe Z;Gd[d\d\eZGdadbdbeZ?GdcddddeZ@Gdedfdfe ZAGdgdhdheZBGdidjdjeZCGdkdldle ZDGdmdndneZEGdodpdpeZFGdqdrdre ZGGdsdtdteZHGdudvdveZIGdwdxdxe ZJGdydzdzeZKGd{d|d|eZLGd}d~d~e ZMGdddeZNGdddeZOGddde ZPGdddeZQGdddeZRGddde ZSGdddeZTGdddeZUGddde ZVGdddeZWGdddeZXGddde ZYGdddeZZGdddeZ[GdddeZ\GdddeZ]Gddde Z^GdddeZ_GdddeZ`Gddde ZaGdddeZbGdddeZcGddde ZdGdddeZeGdddeZfGddde ZgGdddeZhGdddeZiGddde ZjGdddeZkGdddeZlGddde ZmGdddeZnGdd„deZoGddĄde ZpGddƄdeZqGddȄdeZrGddʄde ZsGdd̄deZtGdd΄deZuGddЄde ZvGdd҄deZwGddԄdeZxGddքde ZyGdd؄deZzGddڄdeZ{Gdd܄de Z|GddބdeZ}GdddeZ~Gddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGd d d eZGd d d e ZGd ddeZGdddeZGddde ZGdddeZdS(z4Interfaces to assorted Freesurfer utility programs. N)logging)fname_presuffixsplit_filename) TraitedSpec DirectoryFiletraitsOutputMultiPath isdefined CommandLineCommandLineInputSpec) FSCommand FSTraitedSpecFSSurfaceCommandFSScriptCommandFSScriptOutputSpecFSTraitedSpecOpenMPFSCommandOpenMPZrestructuredtextcormghmgzZmncbrikbshortimgbfloatniiznii.gzgii)rrrmincafnirrspmanalyze analyze4drnifti1rniigzrr r#r$r"r!ZsdtoutlineZotlZgdfr%r&znipype.interfacecCst|s |St|jjr"|jj}ntj}|sHt|jjrD|jj}nd}|dkr\tjj|}|dk rvtjj|||}ntjj||}tjj |stj |tjj||}tjj |st j |||S)z1Method to copy an input to the subjects directory subject_idN)r inputs subjects_dirosgetcwdr(pathbasenamejoinisdirmakedirsisfileshutilcopy)clsin_filefolderr.r(r*out_dirout_filer:D/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/freesurfer/utils.py copy2subjdirMs(         r<cCs<x6t|jD]&}tjj|}tjj|stj|qWdS)zNcreate all output directories. If not created, some freesurfer interfaces failN)listvaluesr+r-dirnamer0r1)outputsoutputr?r:r:r;createoutputdirsns  rBc @seZdZedddddZeddddZejdd dd d d Zej d ddZ dddgZ eddde ddZ ej ddgde ddZej dde ddZejejejejdddZejejejejdd dZej d!dgd"d#Zejd$d%d&dd'd(gd)d*gd+d,Zejejejejejejd-d.Zejd/d0d1d.Zej dd2gd3d4Zejd5d6dZejd7d8dZejd9d:d;dgd?d@ZeddAdBgdCdDZejdEdFdGdHdZej dIdJdZ ej dKd.Z!ej dLdMdZ"ejej ej#dNdOgdPd#Z$ej%dQdOgdRd#Z&ej dSdTgdUd@Z'ej dVdWgdXd@Z(ej%dYdZdZ)ejd[d\dZ*ej%d]d^dZ+ed_dd`daZ,eje-e.dbdcdZ/ejej eddddedfdZ0eje-dgdhdZ1ejej edidjdZ2dkS)lSampleToSurfaceInputSpecTz--mov %szvolume to sample values from)exists mandatoryargstrdescz--ref %sz&reference volume (default is orig.mgz))rDrFrGlhrhz --hemi %sztarget hemisphere)rErFrGz --surf %sz!target surface (default is white))rFrGreg_file reg_header mni152regz--reg %sz%source-to-reference registration file)rDrFrExorrGz--regheader %sr(z!register based on header geometry)rFrequiresrErMrGz --mni152regz source volume is in MNI152 space)rFrErMrGz--rot %.3f %.3f %.3fz3rotation angles (in degrees) to apply to reg matrixz--trans %.3f %.3f %.3fz*translation (in mm) to apply to reg matrixz--srcsubject %sz+override the subject in the reg file header)rFrNrGpointmaxaveragez%sprojection_stemsampling_rangesampling_unitszAhow to sample -- at a point or at the max or average over a range)rErFrMrNrGz7sampling range - a point or a tuple of (min, max, step))rGmmfracz,sampling range type -- either 'mm' or 'frac'sampling_methodz:stem for precomputed linear estimates and volume fractions)rErMrGz --fwhm %.3fzsmooth input volume (mm fwhm)z--surf-fwhm %.3fzsmooth output surface (mm fwhm)ZnearestZ trilinearz --interp %szinterpolation methodz--cortex mask_labelz.mask the target surface with hemi.cortex.label)rFrMrGz --mask %s cortex_maskzlabel file to mask output with)rDrFrMrGroundZ tkregisterz--float2int %sz6method to convert reg matrix values (default is round)z --fixtkregz make reg matrix round-compatiblez subject idz--trgsubject %sz2sample to surface of different subject than sourcez --surfreg %starget_subjectz*use surface registration to target subjectz --icoorder %dz.icosahedron order when target_subject is 'ico'z --reshape no_reshapez/reshape surface vector to fit in non-mgh formatz --noreshapereshapez'do not reshape surface vector (default)z--rf %dz number of 'slices' for reshapingz --scale %.3fz(multiple all intensities by scale factorz --frame %dzsave only one frame (0-based)z--o %szsurface file to write)rFgenfilerGz --out_type %szoutput file type)rDz --srchit %sz,save image with number of hits at each voxelz --srchit_typezhits file typez --nvox %sz>> import nipype.interfaces.freesurfer as fs >>> sampler = fs.SampleToSurface(hemi="lh") >>> sampler.inputs.source_file = "cope1.nii.gz" >>> sampler.inputs.reg_file = "register.dat" >>> sampler.inputs.sampling_method = "average" >>> sampler.inputs.sampling_range = 1 >>> sampler.inputs.sampling_units = "frac" >>> sampler.cmdline # doctest: +ELLIPSIS 'mri_vol2surf --hemi lh --o ...lh.cope1.mgz --reg register.dat --projfrac-avg 1.000 --mov cope1.nii.gz' >>> res = sampler.run() # doctest: +SKIP Z mri_vol2surfc sL|dkr`|jj}|jj}|dkr$d}t|tr8d|}nd|}tdddd |}d |||fS|d krv|j|jjS|d kr|j|jjS|dkr|j|j|S|dkrt |jj r t |j\}}} | t |kr | t j krtdj|| ntjd|| || |tkrdS|dkr8|dkr8|jdStt|j|||S)NrWrUdistz%.3f %.3f %.3fz%.3fz-maxz-avg)rOrPrQz --proj%s%s %srKrkrtrursz'Cannot create {} file with extension {}z(Creating %s file with extension %s: %s%srnTz sphere.reg)rtru)r)rSrT isinstancetupledictrFr(_get_outfilenamer r9rfilemapr> ValueErrorformatloggerwarningrrsuperrw _format_arg) selfnamespecvaluerangeZunitsmethod_baseext) __class__r:r;rOsH         zSampleToSurface._format_argr9cCst|j|}t| s t|trt|jjrX|dkrFdt|jj}qjdt|jj}n|dkrfd}nd}t|jjt j |jj d|dd}|S)Nrtz_hits..z _hits.mgzz.mgzF)newpathprefixsuffixuse_ext) getattrr)r rzboolrsr~rrbr+r,rd)roptoutfilerr:r:r;r}|s    z SampleToSurface._get_outfilenamecCs|jj}tjj|j|d<|jj}t|rL||d<t |t rL|jd}|jj }t|rt |t rt |jj tj|jjdddd}||d<|S)Nr9rtrz_vox.txtF)rrrrru)_outputsgetr+r-abspathr}r)rtr rzrrurrbr,rd)rr@ZhitsfileZvoxfiler:r:r; _list_outputss$     zSampleToSurface._list_outputscCs|dkr|j|SdS)Nr9)r)rrr:r:r; _gen_filenames zSampleToSurface._gen_filename)r9)r_r`ra__doc___cmdrC input_specrv output_specrr}rr __classcell__r:r:)rr;rw,s - rwc@seZdZeddddZejddddZejddd dd d Z ej d d gddZ ej ddgddZ ejdddddZejdddZeddddZdS)SurfaceSmoothInputSpecTz --sval %szsource surface file)rErFrGz--s %szsubject id of surface filerHrIz --hemi %szhemisphere to operate on)rFrErGz --fwhm %.4f smooth_itersz'effective FWHM of the smoothing process)rFrMrGz --smooth %dfwhmz#iterations of the smoothing processz--cortexz)only smooth within ``$hemi.cortex.label``)rF usedefaultrGz --reshapez/reshape surface vector to fit in non-mgh format)rFrGz --tval %szsurface file to write)rFr^rGN)r_r`rar r6r rer(rcrdrjrrorrhcortexr]r9r:r:r:r;rs&  rc@seZdZedddZdS)SurfaceSmoothOutputSpecTzsmoothed surface file)rDrGN)r_r`rar r9r:r:r:r;rsrc@s,eZdZdZdZeZeZddZ ddZ dS) SurfaceSmoothaSmooth a surface image with mri_surf2surf. The surface is smoothed by an interative process of averaging the value at each vertex with those of its adjacent neighbors. You may supply either the number of iterations to run or a desired effective FWHM of the smoothing process. If the latter, the underlying program will calculate the correct number of iterations internally. See Also -------- `nipype.interfaces.freesurfer.utils.SmoothTessellation`_ interface for smoothing a tessellated surface (e.g. in gifti or .stl) Examples -------- >>> import nipype.interfaces.freesurfer as fs >>> smoother = fs.SurfaceSmooth() >>> smoother.inputs.in_file = "lh.cope1.mgz" >>> smoother.inputs.subject_id = "subj_1" >>> smoother.inputs.hemi = "lh" >>> smoother.inputs.fwhm = 5 >>> smoother.cmdline # doctest: +ELLIPSIS 'mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval lh.cope1.mgz --tval ...lh.cope1_smooth5.mgz --s subj_1' >>> smoother.run() # doctest: +SKIP mri_surf2surfcCsh|jj}|jj|d<t|dsd|jj}t|jjrB|jj}n|jj}t|d|t j d|d<|S)Nr9z _smooth%d)rr) rrr)r9r r6rrrr+r,)rr@r6kernelr:r:r;rs     zSurfaceSmooth._list_outputscCs|dkr|j|SdS)Nr9)r)rrr:r:r;rs zSurfaceSmooth._gen_filenameN) r_r`rarrrrrrrrr:r:r:r;rs rc @seZdZeddddgddZeddddgddZejdd d d Zej d d ddddZ ejdddd Z ej dddddddddd Z ej e ddgddZej e ed d!dZejd"d#dZejd$d%dZed&dd'd(Zd)S)*SurfaceTransformInputSpecTz --sval %ssource_annot_filezsurface file with source values)rDrErFrMrGz--sval-annot %srbzsurface annotation filez--srcsubject %szsubject id for source surface)rErFrGrHrIz --hemi %szhemisphere to transform)rFrErGz--trgsubject %szsubject id of target surfacerrrz--trgicoorder %dz3order of the icosahedron if target_subject is 'ico')rFrGz --sfmt %szsource file format)rFrNrGz --tfmt %sz output formatz --reshapez,reshape output surface to conform with Niftiz--reshape-factorz"number of slices in reshaped imagez --tval %szsurface file to write)rFr^rGN)r_r`rar rbrr reZsource_subjectrcrdr[Ztarget_ico_orderrqZ source_typerr target_typerhr]roZreshape_factorr9r:r:r:r;rsP    rc@seZdZedddZdS)SurfaceTransformOutputSpecTztransformed surface file)rDrGN)r_r`rar r9r:r:r:r;r7srcs<eZdZdZdZeZeZfddZ ddZ ddZ Z S) SurfaceTransforma{Transform a surface file from one subject to another via a spherical registration. Both the source and target subject must reside in your Subjects Directory, and they must have been processed with recon-all, unless you are transforming to one of the icosahedron meshes. Examples -------- >>> from nipype.interfaces.freesurfer import SurfaceTransform >>> sxfm = SurfaceTransform() >>> sxfm.inputs.source_file = "lh.cope1.nii.gz" >>> sxfm.inputs.source_subject = "my_subject" >>> sxfm.inputs.target_subject = "fsaverage" >>> sxfm.inputs.hemi = "lh" >>> sxfm.run() # doctest: +SKIP rcs|dkrrt|jjrft|jd\}}}|t|krf|tjkrTtdj||nt j d|||||t krrdSt t |j|||S)Nrr9z'Cannot create {} file with extension {}z(Creating %s file with extension %s: %s%sry)r r)r9rrr~r>rrrrrrrrr)rrrrrrr)rr:r;rSs"    zSurfaceTransform._format_argcCs|jj}|jj|d<t|dst|jjr:|jj}n|jj}dddD}d}t|d|krp|d}d}d}t|jjrdt |jj}d}t |d|jj |ft j |d|d<nt jj|jj|d<|S)Nr9cSsg|] }d|qS)z.%sr:).0er:r:r; usz2SurfaceTransform._list_outputs..areamidpialavg_curvcurvinflatedjacobian_whiteorignofixsmoothwmcrvspheresulc thicknessvolumewhiteTrz.stripmeFryrz.%s%s)rrr)rrrrrrrrrrrrrrrr)rrr)r9r rbrrrr~rr[r+r,r-r)rr@sourceZbad_extensionsrrr:r:r;risL      zSurfaceTransform._list_outputscCs|dkr|j|SdS)Nr9)r)rrr:r:r;rs zSurfaceTransform._gen_filename) r_r`rarrrrrrrrrrr:r:)rr;r;s 2rc@seZdZedddddgddZejdddd Zed d d d gddZedddddgdZ eddddZ ej ddd gdZ edddd gddZ ejdddZejdd dZejd!d"dZejd#d$d%gd&Zd'S)(Surface2VolTransformInputSpecTz --surfval %sFmkmaskz(This is the source of the surface values)rDrFcopyfilerErMrGz --hemi %szhemisphere of data)rFrErGz %s_asVol.niiz Output volumez --outvol %srb) name_templaterGrF name_source hash_filesz --volreg %sz,tkRAS-to-tkRAS matrix (tkregister2 format)r()rDrFrErGrMz --template %szOutput template volume)rDrFrGz-make a mask instead of loading surface valuesz--mkmask)rGrFrMz%s_asVol_vertex.niizPath name of the vertex output volume, which is the same as output volume except that the value of each voxel is the vertex-id that is mapped to that voxel.z --vtxvol %sz --surf %szsurfname (default is white))rFrGz --projfrac %szthickness fractionz--sd %sz7freesurfer subjects directory defaults to $SUBJECTS_DIRz --identity %sz subject idrJ)rFrGrMN)r_r`rar rbr rmrdtransformed_filerJZ template_filerhrvertexvol_fileZ surf_namerjZprojfracr*r(r:r:r:r;rsL   rc@s"eZdZedddZeddZdS)Surface2VolTransformOutputSpecTz$Path to output file if used normally)rDrGz#vertex map volume path id. Optional)rGN)r_r`rar rrr:r:r:r;rs rc@seZdZdZdZeZeZdS)Surface2VolTransformaUse FreeSurfer mri_surf2vol to apply a transform. Examples -------- >>> from nipype.interfaces.freesurfer import Surface2VolTransform >>> xfm2vol = Surface2VolTransform() >>> xfm2vol.inputs.source_file = 'lh.cope1.mgz' >>> xfm2vol.inputs.reg_file = 'register.mat' >>> xfm2vol.inputs.hemi = 'lh' >>> xfm2vol.inputs.template_file = 'cope1.nii.gz' >>> xfm2vol.inputs.subjects_dir = '.' >>> xfm2vol.cmdline 'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii' >>> res = xfm2vol.run()# doctest: +SKIP Z mri_surf2volN) r_r`rarrrrrrr:r:r:r;rsrc @seZdZeddd dddZeddd!dddZedgd ddd"dd d Zedd ddZej dddZ eddddZ eddddZ ej dddZ ejdddZej dddZejdddZdS)#ApplyMaskInputSpecTrz%szinput image (will be masked))rDrEpositionrFrGrzimage defining mask spacer6z %s_maskedrzfinal image to write)rrrkeep_extensionrrFrGz -xform %sz9LTA-format transformation matrix to align mask with input)rDrFrGz-invertzinvert transformation)rFrGz -lta_src %sz%image defining transform source spacez -lta_dst %sz%image defining transform target spacez-absz+take absolute value of mask before applyingz-T %.4fzthreshold mask before applyingz-keep_mask_deletion_editsz=transfer voxel-deletion edits (voxels=1) from mask to out volz -transfer %dz,transfer only voxel value # from mask to outN)r_r`rar r6Z mask_filer9Zxfm_filer rhZ invert_xfmZ xfm_sourceZ xfm_targetZuse_absrjZ mask_threshZkeep_mask_deletion_editsroZtransferr:r:r:r;rsJ   rc@seZdZedddZdS)ApplyMaskOutputSpecTz masked image)rDrGN)r_r`rar r9r:r:r:r;r%src@seZdZdZdZeZeZdS) ApplyMaskzUse Freesurfer's mri_mask to apply a mask to an image. The mask file need not be binarized; it can be thresholded above a given value before application. It can also optionally be transformed into input space with an LTA matrix. Zmri_maskN) r_r`rarrrrrrr:r:r:r;r*src@s"eZdZejdddddZejdddddd dZejd ddd dZej d d dgdZ ej dddgdZ e ddddgdZ dddgZe ddeddZej deddZej d ed!dZejejejejejejejejejd"dd#Zejd$d%d&Zej d'd(d&Zej d)d*d&Zej d+d,d&Zej d-d.d&Ze dd/d0gd1dZejd/d2gd3dZe dd4d5gd6dZejd4d7gd8dZe dd9d:d;Zej dd?d&Z!e dd@dAd;Z"ejdBdCd&Z#ejdDdEd&Z$ej dFdGd&Z%ej dHdId&Z&ej dJdKZ'ejdLdKZ(ej)ejdMgdNdOZ*e ddddPdQZ+dRS)SSurfaceSnapshotsInputSpecrz%sTzsubject to visualize)rrFrErGrHrIrzhemisphere to visualizerzsurface to visualizez-curvzshow curvatureshow_gray_curv)rFrGrMz-grayzshow curvature in gray show_curvz -overlay %szload an overlay volume/surface overlay_range)rDrFrGrN overlay_reg identity_reg mni152_regz-overlay-reg %sz7registration matrix file to register overlay to surface)rDrFrMrGz-overlay-reg-identityz>use the identity matrix to register the overlay to the surface)rFrMrGz -mni152regz>use to display a volume in MNI152 space on the average subjectz8overlay range--either min, (min, max) or (min, mid, max))rGrFz -foffset %.3fz3overlay range will be symettric around offset value)rFrGz-truncphaseflag 1ztruncate the overlay displayz-revphaseflag 1zreverse the overlay displayz-invphaseflag 1zinvert the overlay displayz-zmzremove mean from overlayz-annotation %s annot_namez"path to annotation file to display annot_filezBname of annotation to display (must be in $subject/label directoryz -label %s label_namezpath to label file to display label_filez=name of label to display (must be in $subject/label directoryz-colortable %szload colortable file)rDrFrGz -labels-underz#draw label/annotation under overlayz-label-outlinez draw label/annotation as outlinez -patch %sz load a patchz-orig %sz"set the orig surface suffix stringz -sphere %sz set the sphere.reg suffix stringz-colscalebarflag 1zdisplay the color scale barz-colscaletext 1z#display text in the color scale barz*also take anterior and posterior snapshots)rGz%stem to use for screenshot file namesscreenshot_stemzCinput names to use as arguments for a string-formated stem template)rNrGz"override default screenshot script)rDrFr^rGN),r_r`rar rer(rcrdrfrhrrr ZoverlayrgrrrrlrjrirZoverlay_range_offsetZtruncate_overlayZreverse_overlayZinvert_overlayZdemean_overlayrrrrZ colortableZ label_underZ label_outlineZ patch_fileZ orig_suffixZ sphere_suffixZshow_color_scaleZshow_color_text six_imagesrListstem_template_args tcl_scriptr:r:r:r;r8s             rc@seZdZeeddddZdS)SurfaceSnapshotsOutputSpecT)rDz6tiff images of the surface from different perspectives)rGN)r_r`rar r snapshotsr:r:r:r;rsrcsPeZdZdZdZeZeZfddZ fddZ ddZ d d Z d d Z ZS) SurfaceSnapshotsaUse Tksurfer to save pictures of the cortical surface. By default, this takes snapshots of the lateral, medial, ventral, and dorsal surfaces. See the ``six_images`` option to add the anterior and posterior surfaces. You may also supply your own tcl script (see the Freesurfer wiki for information on scripting tksurfer). The screenshot stem is set as the environment variable "_SNAPSHOT_STEM", which you can use in your own scripts. Node that this interface will not run if you do not have graphics enabled on your system. Examples -------- >>> import nipype.interfaces.freesurfer as fs >>> shots = fs.SurfaceSnapshots(subject_id="fsaverage", hemi="lh", surface="pial") >>> shots.inputs.overlay = "zstat1.nii.gz" >>> shots.inputs.overlay_range = (2.3, 6) >>> shots.inputs.overlay_reg = "register.dat" >>> res = shots.run() # doctest: +SKIP Ztksurfercs|dkrt|sdSd|Sn|dkrht|tr8d|St|dkrLd|Sd|d |d|d fSnV|d krt|r|jd r|dd}tjd|jj|ddr|dd}d|St t |j |||S)Nrz-tcl snapshots.tclz-tcl %srz -fthresh %.3frz-fminmax %.3f %.3fz-fminmax %.3f %.3f -fmid %.3frrrz.annotrz %s[\.\-_]rz-annotation %si) r rzfloatlenendswithrematchr)rdrrr)rrrr)rr:r;rs(      zSurfaceSnapshots._format_argcstjjs(djjjjjjf}n6jj}jj}t|r^tfdd|D}||}dtj krpt d||j d<j t t j|}ddg}x |D]}||jkrj|qWd |_|S) Nz%s_%s_%scsg|]}tj|qSr:)rr))rarg)rr:r;r sz3SurfaceSnapshots._run_interface..ZDISPLAYz/Graphics are not enabled -- cannot run tksurferZ_SNAPSHOT_STEMz)surfer: failed, no suitable display foundz3Fatal Error in tksurfer.bin: could not open displayr)r r)rr(rdrfrr{r+environ RuntimeError_write_tcl_scriptrr_run_interfacestderrraise_exception returncode)rruntimestem stem_argsargserrorserr)r)rr;rs,     zSurfaceSnapshots._run_interfacec Cs|tdd}ddddddddd dd dd g }t|jjrV|jjrV|jdd dd ddddg|jd|jdj||jdS)Nz snapshots.tclwz&save_tiff $env(_SNAPSHOT_STEM)-lat.tifZmake_lateral_viewzrotate_brain_y 180Zredrawz&save_tiff $env(_SNAPSHOT_STEM)-med.tifzrotate_brain_x 90z&save_tiff $env(_SNAPSHOT_STEM)-ven.tifzrotate_brain_x -90z&save_tiff $env(_SNAPSHOT_STEM)-dor.tifzrotate_brain_y 90z&save_tiff $env(_SNAPSHOT_STEM)-pos.tifzrotate_brain_y -90z&save_tiff $env(_SNAPSHOT_STEM)-ant.tifexit ) openr r)rextendappendwriter/close)rZfidscriptr:r:r;r"s6  z"SurfaceSnapshots._write_tcl_scriptcsjj}tjjs4djjjjjjfn6jjjj}t|rjt fdd|D}|ddddg}jj r|j dd gfd d|D}||d <|S) Nz%s_%s_%scsg|]}tj|qSr:)rr))rr)rr:r;rQsz2SurfaceSnapshots._list_outputs..z %s-lat.tifz %s-med.tifz %s-dor.tifz %s-ven.tifz %s-pos.tifz %s-ant.tifcsg|]}j|ddqS)ry)r) _gen_fname)rf)rrr:r;rVsr) rrr r)rr(rdrfrr{rr)rr@rrrr:)rrr;rEs"   zSurfaceSnapshots._list_outputscCs|dkr dSdS)Nrz snapshots.tclr:)rrr:r:r;rZszSurfaceSnapshots._gen_filename)r_r`rarrrrrrrrrrrrr:r:)rr;rs  "#rc@seZdZedddddZdS)ImageInfoInputSpecTrz%szimage to query)rDrrFrGN)r_r`rar r6r:r:r:r;r `sr c@seZdZejddZedddZejddZ ejddZ ejddZ ejd dZ ejd dZ ejd dZejd dZejd dZejddZdS)ImageInfoOutputSpeczoutput of mri_info)rGTz text file with image information)rDrGzimage data typez file formatzecho time (msec)zrepetition time(msec)zinversion time (msec)zimage dimensions (voxels)zvoxel sizes (mm)zimage orientationzphase encode directionN)r_r`rar ZAnyinfor r9re data_type file_formatTETRTIri dimensions vox_sizes orientation ph_enc_dirr:r:r:r;r es          r c@s,eZdZdZeZeZdddZd ddZ dS) ImageInfoZmri_inforcCs*tjd||f|}|r"|jdSdSdS)Nz%s\s*:\s+(.+?)%sr)rsearchgroup)rr fielddelimmr:r:r; info_regexpzs zImageInfo.info_regexpNc Cs|j}|j}||_x.z x Z OrientationZPhEncDirz%s\s*:\s+(.+?)\ntype)rrr)rstdoutr rrsetattrr{splitrrrrrfindallrr) rrZneeded_outputsr@r rZfieldvalZvoxZdimZftypeZdtyper:r:r;aggregate_outputss(     zImageInfo.aggregate_outputs)r)NN) r_r`rarr rr rrr&r:r:r:r;rts  rc @sHeZdZdZeddddZeddddZeddd dZedd d dZedd d dZ eddddZ e j dddZ e j dddZe j dddZe j dddZe j dddZe jdddZe jdddZe jd d!dZe jd"d#dZedddMRIsConvertInputSpeczT Uses Freesurfer's mris_convert to convert surface files to various formats Tz --annot %sz'input is annotation or gifti label data)rDrFrGz--parcstats %sz6infile is name of text file containing label/val pairsz --label %sz2infile is .label file, label is name of this labelz-c %sz>input is scalar curv overlay file (must still specify surface)z-f %szPinput is functional time-series or other multi-frame data (must specify surface)Fz--labelstats %szBoutfile is name of gifti file to which label stats will be writtenz-pz$input is a patch, not a full surface)rFrGz-rz9rescale vertex xyz so total area is same as group averagez-nz)output is an ascii file where vertex dataz-az$Print only surface xyz to ascii filez-vz,Writes out neighbors of a vertex in each rowz-s %.3fzscale vertex xyz by scalez --da_num %dz:if input is gifti, 'num' specifies which data array to usez-t %sz,apply talairach xfm of subject to vertex xyzz-o %szread orig positionsrz%szFile to read/convert)rDrErrFrGr out_datatypez'output filename or True to generate one)rFrr^rMrErGZascZicoZtristlZvtkrrrr9zThese file formats are supported: ASCII: .ascICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded 'volume': .mgh, .mgz)rMrErGz --to-scannerzAconvert coordinates from native FS (tkr) coords to scanner coordsz--to-tkrzAconvert coordinates from scanner coords to native FS (tkr) coordsNrr)r_r`rarr rparcstats_filerscalarcurv_filefunctional_fileZlabelstats_outfiler rhpatchZrescaleZnormalZ xyz_asciiZvertexrjZscaleroZ dataarray_numreZtalairachxfm_subjidZorignamer6r9rcr(Z to_scannerZto_tkrr:r:r:r;r's    r'c@seZdZdZedddZdS)MRIsConvertOutputSpeczT Uses Freesurfer's mris_convert to convert surface files to various formats Tzconverted output surface)rDrGN)r_r`rarr convertedr:r:r:r;r.sr.csDeZdZdZdZeZeZfddZ ddZ ddZ d d Z Z S) MRIsConverta5 Uses Freesurfer's mris_convert to convert surface files to various formats Example ------- >>> import nipype.interfaces.freesurfer as fs >>> mris = fs.MRIsConvert() >>> mris.inputs.in_file = 'lh.pial' >>> mris.inputs.out_datatype = 'gii' >>> mris.run() # doctest: +SKIP mris_convertcs6|dkr"tjj| r"tjj|}tt|j|||S)Nr9)r+r-isabsrrr0r)rrrr)rr:r;rs zMRIsConvert._format_argcCs$|jj}tjj|j|d<|S)Nr/)rrr+r-r_gen_outfilename)rr@r:r:r;r#s zMRIsConvert._list_outputscCs |dkrtjj|jSdSdS)Nr9)r+r-rr3)rrr:r:r;r(szMRIsConvert._gen_filenamecCst|jjr|jjSt|jjr4t|jj\}}}nt|jjrTt|jj\}}}n~t|jjrtt|jj\}}}n^t|jjrt|jj\}}}n>t|jjrt|jj\}}}nt|jj rt|jj \}}}||d|jj S)Nz _converted.) r r)r9rrr*rr+r,r6r()rrrrr:r:r;r3.s       zMRIsConvert._gen_outfilename)r_r`rarrr'rr.rrrrr3rr:r:)rr;r0 s  r0c @s@eZdZdZejedddddddddZed d ddd d Zd S)MRIsCombineInputSpeczO Uses Freesurfer's mris_convert to combine two surface files into one. T)ZExistsrrz--combinesurfs %szTwo surfaces to be combined.)maxlenZminlenrErrFrGz%sz1Output filename. Combined surfaces from in_files.)rFrr^rErGNr) r_r`rarr rr Zin_filesr9r:r:r:r;r4Asr4c@seZdZdZedddZdS)MRIsCombineOutputSpeczO Uses Freesurfer's mris_convert to combine two surface files into one. Tz1Output filename. Combined surfaces from in_files.)rDrGN)r_r`rarr r9r:r:r:r;r6Xsr6c@s,eZdZdZdZeZeZddZ ddZ dS) MRIsCombineaI Uses Freesurfer's ``mris_convert`` to combine two surface files into one. For complete details, see the `mris_convert Documentation. `_ If given an ``out_file`` that does not begin with ``'lh.'`` or ``'rh.'``, ``mris_convert`` will prepend ``'lh.'`` to the file name. To avoid this behavior, consider setting ``out_file = './'``, or leaving out_file blank. In a Node/Workflow, ``out_file`` is interpreted literally. Example ------- >>> import nipype.interfaces.freesurfer as fs >>> mris = fs.MRIsCombine() >>> mris.inputs.in_files = ['lh.pial', 'rh.pial'] >>> mris.inputs.out_file = 'bh.pial' >>> mris.cmdline 'mris_convert --combinesurfs lh.pial rh.pial bh.pial' >>> mris.run() # doctest: +SKIP r1cCs^|jj}tjj|jj\}}|dkr@|dddkr@d|}tjjtjj|||d<|S)Nryrlh.rh.r9)r8r9) rrr+r-r$r)r9rr/)rr@r-rr:r:r;rs  zMRIsCombine._list_outputscCs$t|jjr tjj|jj|j_dS)z Filename normalization routine to perform only when run in Node context. Interpret out_file as a literal path to reduce surprise. N)r r)r9r+r-r)rr:r:r;normalize_filenamess zMRIsCombine.normalize_filenamesN) r_r`rarrr4rr6rrr:r:r:r:r;r7bs  r7c@s`eZdZdZeddddddZejdddd d Zedddd d Z ej dddZ ej dddZ dS)MRITessellateInputSpeczb Uses Freesurfer's mri_tessellate to create surfaces by tessellating a given input volume Trz%sz&Input volume to tesselate voxels from.)rDrErrFrGrz%dzvLabel value which to tesselate from the input volume. (integer, if input is "filled.mgz" volume, 127 is rh, 255 is lh))rrFrErGrz'output filename or True to generate one)rFrr^rGz-az:Tessellate the surface of all voxels with different labels)rFrGz-nz>> import nipype.interfaces.freesurfer as fs >>> tess = fs.MRITessellate() >>> tess.inputs.in_file = 'aseg.mgz' >>> tess.inputs.label_value = 17 >>> tess.inputs.out_file = 'lh.hippocampus' >>> tess.run() # doctest: +SKIP Zmri_tessellatecCs$|jj}tjj|j|d<|S)Nrf)rrr+r-rr3)rr@r:r:r;rs zMRITessellate._list_outputscCs|dkr|jSdSdS)Nr9)r3)rrr:r:r;rszMRITessellate._gen_filenamecCsBt|jjr|jjSt|jj\}}}||dt|jjSdS)Nr)r r)r9rr6strr<)rrrrr:r:r;r3s zMRITessellate._gen_outfilenameN) r_r`rarrr;rr=rrrr3r:r:r:r;r>s r>c @seZdZeddddddZejejdejddddddd d Z eddddd dZ eddd gddddZ ej ddddZ ej ddddZej ddddZdS)MRIPretessInputSpecTrz%szfilled volume, usually wm.mgz)rDrErrFrGwmrrznlabel to be picked up, can be a Freesurfer's string like 'wm' or a label value (e.g. 127 for rh or 255 for lh))rFdefaultrErrrGrz;the normalized, brain-extracted T1w image. Usually norm.mgz in_filledz %s_pretesswmz"the output file after mri_pretess.)rrFrrrrGFz -nocornersz=do not remove corner configurations in addition to edge ones.)rFrGz-keepz keep WM editsz-testzadds a voxel that should be removed by mri_pretess. The value of the voxel is set to that of an ON-edited WM, so it should be kept with -keep. The output will NOT be saved.Nrrr)r_r`rar rCr rlrmrolabelZin_normr9rhZ nocornersZkeeptestr:r:r:r;r@sJr@c@seZdZedddZdS)MRIPretessOutputSpecTzoutput file after mri_pretess)rDrGN)r_r`rar r9r:r:r:r;rGsrGc@seZdZdZdZeZeZdS) MRIPretessaV Uses Freesurfer's mri_pretess to prepare volumes to be tessellated. Changes white matter (WM) segmentation so that the neighbors of all voxels labeled as WM have a face in common - no edges or corners allowed. Example ------- >>> import nipype.interfaces.freesurfer as fs >>> pretess = fs.MRIPretess() >>> pretess.inputs.in_filled = 'wm.mgz' >>> pretess.inputs.in_norm = 'norm.mgz' >>> pretess.inputs.nocorners = True >>> pretess.cmdline 'mri_pretess -nocorners wm.mgz wm norm.mgz wm_pretesswm.mgz' >>> pretess.run() # doctest: +SKIP Z mri_pretessN) r_r`rarrr@rrGrr:r:r:r;rHsrHc@sXeZdZdZeddddddZejdddd d Zejddddd d Z ed ddddZ dS)MRIMarchingCubesInputSpeczZ Uses Freesurfer's mri_mc to create surfaces by tessellating a given input volume Trz%sz&Input volume to tesselate voxels from.)rDrErrFrGrz%dzvLabel value which to tesselate from the input volume. (integer, if input is "filled.mgz" volume, 127 is rh, 255 is lh))rrFrErGzEAlter the marching cubes connectivity: 1=6+,2=18,3=6,4=26 (default=1))rrFrrGz./%sz'output filename or True to generate one)rFrr^rGNrr) r_r`rarr r6r ror<Zconnectivity_valuer9r:r:r:r;rI9s.rIc@seZdZdZedddZdS)MRIMarchingCubesOutputSpeczZ Uses Freesurfer's mri_mc to create surfaces by tessellating a given input volume Tz#binary surface of the tessellation )rDrGN)r_r`rarr rfr:r:r:r;rJZsrJc@s4eZdZdZdZeZeZddZ ddZ ddZ d S) MRIMarchingCubesac Uses Freesurfer's mri_mc to create surfaces by tessellating a given input volume Example ------- >>> import nipype.interfaces.freesurfer as fs >>> mc = fs.MRIMarchingCubes() >>> mc.inputs.in_file = 'aseg.mgz' >>> mc.inputs.label_value = 17 >>> mc.inputs.out_file = 'lh.hippocampus' >>> mc.run() # doctest: +SKIP Zmri_mccCs|jj}|j|d<|S)Nrf)rrr3)rr@r:r:r;rus  zMRIMarchingCubes._list_outputscCs|dkr|jSdSdS)Nr9)r3)rrr:r:r;rzszMRIMarchingCubes._gen_filenamecCsRt|jjrtjj|jjSt|jj\}}}tjj||dt|jj SdS)Nr) r r)r9r+r-rrr6r?r<)rrrrr:r:r;r3s z!MRIMarchingCubes._gen_outfilenameN) r_r`rarrrIrrJrrrr3r:r:r:r;rKbs rKc@seZdZedddd!dddZejdddZejd d dZejd d dZ ej d ddZ ejdddZ ejdddZ ej dddZej dddZej dddZedd"dddZedddZedddZejdddZd S)#SmoothTessellationInputSpecTz%srz&Input volume to tesselate voxels from.)rDrErFrrrGz-a %dz5Number of curvature averaging iterations (default=10))rFrGz-n %dz+Number of smoothing iterations (default=10)z-w %dz#Write snapshot every *n* iterationsz-gz Use Gaussian curvature smoothingz%dz %dz-nwz4Disables the writing of curvature and area estimatesz-areaz#Normalizes the area after smoothingz-mz Uses momentumrz'output filename or True to generate one)rFrr^rGz-c %sz3Write curvature to ``?h.curvname`` (default "curv")z-b %sz.Write area to ``?h.areaname`` (default "area")z-seed %dz(Seed for setting random number generatorNrr)r_r`rar r6r roZcurvature_averaging_iterationsZsmoothing_iterationsZsnapshot_writing_iterationsrhZ use_gaussian_curvature_smoothingZgaussian_curvature_norm_stepsZ"gaussian_curvature_smoothing_stepsZdisable_estimatesZnormalize_areaZ use_momentumr9Zout_curvature_fileZ out_area_fileseedr:r:r:r;rLsF          rLc@seZdZdZedddZdS)SmoothTessellationOutputSpeczP This program smooths the tessellation of a surface using 'mris_smooth' TzSmoothed surface file.)rDrGN)r_r`rarr rfr:r:r:r;rNsrNcsDeZdZdZdZeZeZddZ ddZ ddZ fd d Z Z S) SmoothTessellationa Smooth a tessellated surface. See Also -------- `nipype.interfaces.freesurfer.utils.SurfaceSmooth`_ interface for smoothing a scalar field along a surface manifold Example ------- >>> import nipype.interfaces.freesurfer as fs >>> smooth = fs.SmoothTessellation() >>> smooth.inputs.in_file = 'lh.hippocampus.stl' >>> smooth.run() # doctest: +SKIP Z mris_smoothcCs|jj}|j|d<|S)Nrf)rrr3)rr@r:r:r;rs  z SmoothTessellation._list_outputscCs|dkr|jSdSdS)Nr9)r3)rrr:r:r;rsz SmoothTessellation._gen_filenamecCsFt|jjrtjj|jjSt|jj\}}}tjj|d|SdS)N _smoothed)r r)r9r+r-rrr6)rrrrr:r:r;r3s z#SmoothTessellation._gen_outfilenamecs(tt|j|}d|jkr$|j||S)Nfailed)rrOrrr)rr)rr:r;rs  z!SmoothTessellation._run_interface)r_r`rarrrLrrNrrrr3rrr:r:)rr;rOsrOc@s4eZdZejejdddddZeddddd Zd S) MakeAverageSubjectInputSpecz --subjects %sz"freesurfer subjects ids to averageT )rFrGrEseprQz--out %szname for the average subject)rFrGrN) r_r`rar rrmZ subjects_idsr out_namer:r:r:r;rRsrRc@seZdZejddZdS)MakeAverageSubjectOutputSpeczOutput registration file)rGN)r_r`rar rmaverage_subject_namer:r:r:r;rVsrVc@s$eZdZdZdZeZeZddZ dS)MakeAverageSubjectaMake an average freesurfer subject Examples -------- >>> from nipype.interfaces.freesurfer import MakeAverageSubject >>> avg = MakeAverageSubject(subjects_ids=['s1', 's2']) >>> avg.cmdline 'make_average_subject --out average --subjects s1 s2' Zmake_average_subjectcCs|jj}|jj|d<|S)NrW)rrr)rU)rr@r:r:r;rs  z MakeAverageSubject._list_outputsN) r_r`rarrrRrrVrrr:r:r:r;rX s  rXc@s0eZdZeddddddZeddddd d Zd S) ExtractMainComponentInputSpecTz%srzinput surface file)rDrErFrrGz %s.maincmpr6rz!surface containing main component)rrrFrrGN)r_r`rar r6r9r:r:r:r;rY#srYc@seZdZedddZdS)ExtractMainComponentOutputSpecTz!surface containing main component)rDrGN)r_r`rar r9r:r:r:r;rZ0srZc@seZdZdZdZeZeZdS)ExtractMainComponentaExtract the main component of a tesselated surface Examples -------- >>> from nipype.interfaces.freesurfer import ExtractMainComponent >>> mcmp = ExtractMainComponent(in_file='lh.pial') >>> mcmp.cmdline 'mris_extract_main_component lh.pial lh.maincmp' Zmris_extract_main_componentN) r_r`rarrrYrrZrr:r:r:r;r[4s r[c@seZdZedddgddZejdddgd d Zeddd d d ZeddddZ eddddZ eddddZ ejdgddZ ej dedddZej dedddZejddgddZejdddZejdd dd!d"Zed#ddd$d%d&Zejdd'd(dZejdd)dd*d+gd,d Zejd-d.dZd/S)0Tkregister2InputSpecTz --targ %sfstargz target volume)rDrFrMrGFz--fstarg target_imagezuse subject's T1 as reference)rFrMrGz--mov %sz moving volume)rDrErFrGz--fsl %sz#fsl-style registration input matrix)rDrFrGz--xfm %sz7use a matrix in MNI coordinates as initial registrationz--lta %slta_inz Invert input LTA before applying)rNrGz--fslregout %sz-compute an FSL-compatible resgitration matrix)rFrGz --ltaout %sz%output registration file (LTA format)z --ltaout-inv)rFrNrGz--s %szfreesurfer subject IDz--noeditzdo not open edit window (exit))rFrrGz register.datz--reg %sz"freesurfer-style registration file)rrErFrGz --regheaderz compute regstration from headersz--fstal moving_imagerJz'set mov to be tal and reg to be tal xfmz --movscale %fz'adjust registration matrix to scale movN)r_r`rar r^r rhr]r`Z fsl_in_matrixZxfmr_ invert_lta_inrlfsl_outlta_outZinvert_lta_outrer(ZnoeditrJrKZfstalrjZmovscaler:r:r:r;r\Fsd   r\c@s,eZdZedddZeddZeddZdS)Tkregister2OutputSpecTz"freesurfer-style registration file)rDrGzFSL-style registration file)rGzLTA-style registration fileN)r_r`rar rJfsl_filelta_filer:r:r:r;rds  rdcs<eZdZdZdZeZeZfddZ ddZ ddZ Z S) Tkregister2a Examples -------- Get transform matrix between orig (*tkRAS*) and native (*scannerRAS*) coordinates in Freesurfer. Implements the first step of mapping surfaces to native space in `this guide `__. >>> from nipype.interfaces.freesurfer import Tkregister2 >>> tk2 = Tkregister2(reg_file='T1_to_native.dat') >>> tk2.inputs.moving_image = 'T1.mgz' >>> tk2.inputs.target_image = 'structural.nii' >>> tk2.inputs.reg_header = True >>> tk2.cmdline 'tkregister2 --mov T1.mgz --noedit --reg T1_to_native.dat --regheader --targ structural.nii' >>> tk2.run() # doctest: +SKIP The example below uses tkregister2 without the manual editing stage to convert FSL-style registration matrix (.mat) to FreeSurfer-style registration matrix (.dat) >>> from nipype.interfaces.freesurfer import Tkregister2 >>> tk2 = Tkregister2() >>> tk2.inputs.moving_image = 'epi.nii' >>> tk2.inputs.fsl_in_matrix = 'flirt.mat' >>> tk2.cmdline 'tkregister2 --fsl flirt.mat --mov epi.nii --noedit --reg register.dat' >>> tk2.run() # doctest: +SKIP Z tkregister2csD|dkr|jjrd}|dkr0|dkr0|j|}tt|j|||S)Nr_z --lta-inv %srbrcT)rbrc)r)rarrrgr)rrrr)rr:r;rs  zTkregister2._format_argcCs|jj}tjj|jj}||d<tj}|jj}t |rn|dkrZt |d|dd|d<ntjj|jj|d<|jj }t |r|dkrt |d|dd|d<ntjj|jj |d<|S) NrJTz.matF)rrrrez.ltarf) rrr+r-rr)rJr,rbr rrc)rr@rJcwdrbrcr:r:r;rs" zTkregister2._list_outputscCsFt|jjrtjj|jjSt|jj\}}}tjj|d|SdS)NrP)r r)r9r+r-rrr6)rrrrr:r:r;r3s zTkregister2._gen_outfilename) r_r`rarrr\rrdrrrr3rr:r:)rr;rgs rgc@s^eZdZeddddddZeddddddZed dddd d Zejd ddZ ejdddZ dS)AddXFormToHeaderInputSpecTrz%sz input volume)rDrErrFrGFrzxfm filez output.mgzrz output volume)rrFrrGz-cz.do not try to load the xfmfile, just copy name)rFrGz-vz be verboseNrrr) r_r`rar r6 transformr9r rhZ copy_nameverboser:r:r:r;ris ric@seZdZedddZdS)AddXFormToHeaderOutputSpecTz output volume)rDrGN)r_r`rar r9r:r:r:r;rlsrlcs4eZdZdZdZeZeZfddZ ddZ Z S)AddXFormToHeadera" Just adds specified xform to the volume header. .. danger :: Input transform **MUST** be an absolute path to a DataSink'ed transform or the output will reference a transform in the workflow cache directory! Examples -------- >>> from nipype.interfaces.freesurfer import AddXFormToHeader >>> adder = AddXFormToHeader() >>> adder.inputs.in_file = 'norm.mgz' >>> adder.inputs.transform = 'trans.mat' >>> adder.cmdline 'mri_add_xform_to_header trans.mat norm.mgz output.mgz' >>> adder.inputs.copy_name = True >>> adder.cmdline 'mri_add_xform_to_header -c trans.mat norm.mgz output.mgz' >>> adder.run() # doctest: +SKIP References ---------- [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header] Zmri_add_xform_to_headercs |dkr |Stt|j|||S)Nrj)rrmr)rrrr)rr:r;rszAddXFormToHeader._format_argcCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;r"s zAddXFormToHeader._list_outputs) r_r`rarrrirrlrrrrr:r:)rr;rms  rmc@sJeZdZeddgdddddZejddgddd d Zejd dd ddZ dS) CheckTalairachAlignmentInputSpecz-xfm %ssubjectTrz'specify the talairach.xfm file to check)rFrMrDrErrGz-subj %sr6zspecify subject's name)rFrMrErrGg{Gz?z-T %.3fz5Talairach transforms for subjects with p-values <= T z-are considered as very unlikely default=0.010) default_valuerrFrGNrrzbTalairach transforms for subjects with p-values <= T are considered as very unlikely default=0.010) r_r`rar r6r rerorj thresholdr:r:r:r;rn(s&rnc@seZdZedddZdS)!CheckTalairachAlignmentOutputSpecTz*The input file for CheckTalairachAlignment)rDrGN)r_r`rar r9r:r:r:r;rrBsrrc@s$eZdZdZdZeZeZddZ dS)CheckTalairachAlignmenta This program detects Talairach alignment failures Examples ======== >>> from nipype.interfaces.freesurfer import CheckTalairachAlignment >>> checker = CheckTalairachAlignment() >>> checker.inputs.in_file = 'trans.mat' >>> checker.inputs.threshold = 0.005 >>> checker.cmdline 'talairach_afd -T 0.005 -xfm trans.mat' >>> checker.run() # doctest: +SKIP Z talairach_afdcCs|jj}|jj|d<|S)Nr9)rrr)r6)rr@r:r:r;r\s  z%CheckTalairachAlignment._list_outputsN) r_r`rarrrnrrrrrr:r:r:r;rsFs rsc@s:eZdZedddddZedddddZejd d d Zd S) TalairachAVIInputSpecz--i %sTz input volume)rFrDrErGz--xfm %sFzoutput xfm file)rFrErDrGz --atlas %sz2alternate target atlas (in freesurfer/average dir))rFrGN) r_r`rar r6r9r reatlasr:r:r:r;rtbs rtc@s0eZdZedddZedddZedddZdS)TalairachAVIOutputSpecFz%The output transform for TalairachAVI)rDrGz$The output log file for TalairachAVIz%The output text file for TaliarachAVIN)r_r`rar r9out_logout_txtr:r:r:r;rvms  rvc@s$eZdZdZdZeZeZddZ dS) TalairachAVIa{ Front-end for Avi Snyders image registration tool. Computes the talairach transform that maps the input volume to the MNI average_305. This does not add the xfm to the header of the input file. When called by recon-all, the xfm is added to the header after the transform is computed. Examples ======== >>> from nipype.interfaces.freesurfer import TalairachAVI >>> example = TalairachAVI() >>> example.inputs.in_file = 'norm.mgz' >>> example.inputs.out_file = 'trans.mat' >>> example.cmdline 'talairach_avi --i norm.mgz --xfm trans.mat' >>> example.run() # doctest: +SKIP Z talairach_avicCsb|jj}tjj|jj|d<tjjd|d<tjjtjj|jjdt |jj d|d<|S)Nr9ztalairach_avi.logrwZ talsrcimg_to_zt4_vox2vox.txtrx) rrr+r-rr)r9r/r?r?ru)rr@r:r:r;rs zTalairachAVI._list_outputsN) r_r`rarrrtrrvrrr:r:r:r;ryss ryc@seZdZeddddddZdS)TalairachQCInputSpecz%sTrzThe log file for TalairachQC)rFrErDrrGN)r_r`rar log_filer:r:r:r;rzs rzc@seZdZdZdZeZeZdS) TalairachQCz Examples ======== >>> from nipype.interfaces.freesurfer import TalairachQC >>> qc = TalairachQC() >>> qc.inputs.log_file = 'dirs.txt' >>> qc.cmdline 'tal_QC_AZS dirs.txt' Z tal_QC_AZSN) r_r`rarrrzrrrr:r:r:r;r|s r|c @sjeZdZeddddddZedddgddddd d Zeddddd dZeddddddZej dddZ dS)RemoveNeckInputSpecz%sTrzInput file for RemoveNeck)rFrDrErrGFr6z %s_noneckrzOutput file for RemoveNeck)rFrDrrrrrrGrz#Input transform file for RemoveNeckrz"Input template file for RemoveNeckz -radius %dZRadius)rFrGNrDrrr) r_r`rar r6r9rjtemplater roZradiusr:r:r:r;r}s8r}c@seZdZedddZdS)RemoveNeckOutputSpecFzOutput file with neck removed)rDrGN)r_r`rar r9r:r:r:r;rsrc@s,eZdZdZdZeZeZddZ ddZ dS) RemoveNecka Crops the neck out of the mri image Examples ======== >>> from nipype.interfaces.freesurfer import TalairachQC >>> remove_neck = RemoveNeck() >>> remove_neck.inputs.in_file = 'norm.mgz' >>> remove_neck.inputs.transform = 'trans.mat' >>> remove_neck.inputs.template = 'trans.mat' >>> remove_neck.cmdline 'mri_remove_neck norm.mgz trans.mat trans.mat norm_noneck.mgz' Zmri_remove_neckcCs|dkrtjjdSdS)Nr9z nu_noneck.mgz)r+r-r)rrr:r:r;r s zRemoveNeck._gen_fnamecCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;rs zRemoveNeck._list_outputsN) r_r`rarrr}rrrr rr:r:r:r;rs rc@sXeZdZeddddddZeddddddZed dd d Zed dd d ZedddZdS)MRIFillInputSpecz%sTrzInput white matter file)rFrErDrrGFrz*Output filled volume file name for MRIFillz-segmentation %sz#Input segmentation file for MRIFill)rFrDrGz -xform %sz Input transform file for MRIFillz-a %szOutput log file for MRIFill)rFrGNrr) r_r`rar r6r9Z segmentationrjr{r:r:r:r;rs& rc@s"eZdZedddZeddZdS)MRIFillOutputSpecFzOutput file from MRIFill)rDrGzOutput log file from MRIFill)rGN)r_r`rar r9r{r:r:r:r;r s rc@s$eZdZdZdZeZeZddZ dS)MRIFilla This program creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation. Examples ======== >>> from nipype.interfaces.freesurfer import MRIFill >>> fill = MRIFill() >>> fill.inputs.in_file = 'wm.mgz' # doctest: +SKIP >>> fill.inputs.out_file = 'filled.mgz' # doctest: +SKIP >>> fill.cmdline # doctest: +SKIP 'mri_fill wm.mgz filled.mgz' Zmri_fillcCsD|jj}tjj|jj|d<t|jjr@tjj|jj|d<|S)Nr9r{) rrr+r-rr)r9r r{)rr@r:r:r;r, s   zMRIFill._list_outputsN) r_r`rarrrrrrrr:r:r:r;r s  rc @s\eZdZedddddddZeddddgd ddd d Zedd gd dZejddgddZ dS)MRIsInflateInputSpecz%srTzInput file for MRIsInflate)rFrrErDrrGrFr6z %s.inflatedzOutput file for MRIsInflate)rFrrDrrrrrG no_save_sulczOutput sulc file)rDrMrGz -no-save-sulcout_sulczDo not save sulc file as output)rFrMrGNrr) r_r`rar r6r9rr rhrr:r:r:r;r4 s&rc@s$eZdZedddZedddZdS)MRIsInflateOutputSpecFzOutput file for MRIsInflate)rDrGzOutput sulc fileN)r_r`rar r9rr:r:r:r;rN s rc@s$eZdZdZdZeZeZddZ dS) MRIsInflateac This program will inflate a cortical surface. Examples ======== >>> from nipype.interfaces.freesurfer import MRIsInflate >>> inflate = MRIsInflate() >>> inflate.inputs.in_file = 'lh.pial' >>> inflate.inputs.no_save_sulc = True >>> inflate.cmdline # doctest: +SKIP 'mris_inflate -no-save-sulc lh.pial lh.inflated' Z mris_inflatecCs@|jj}tjj|jj|d<|jjs>> from nipype.interfaces.freesurfer import Sphere >>> sphere = Sphere() >>> sphere.inputs.in_file = 'lh.pial' >>> sphere.cmdline 'mris_sphere lh.pial lh.sphere' Z mris_spherecCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;r s zSphere._list_outputsN) r_r`rarrrrrrrr:r:r:r;r s  rc@seZdZeddddZeddddZeddddZeddddZej dddd d Z ej d ddddd dZ ej dddZ ejdddZej dddZej dddZedddZdS) FixTopologyInputSpecTz)Undocumented input file .orig)rDrErGz-Undocumented input file .inflatedzImplicit input brain.mgzzImplicit input wm.mgzrz%szHemisphere being processed)rrFrErGr(rzSubject being processed)rrFrErrGz'If running as a node, set this to True z,otherwise, the topology fixing will be done z in place.)rErGz-seed %dz(Seed for setting random number generator)rFrGz-gazGNo documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.eduz-mgzz -sphere %szSphere input fileNrrzSIf running as a node, set this to True otherwise, the topology fixing will be done z\If running as a node, set this to True otherwise, the topology fixing will be done in place.)r_r`rar in_orig in_inflatedin_brainin_wmr re hemispherer(rh copy_inputsrorMgarrr:r:r:r;r s:  rc@seZdZedddZdS)FixTopologyOutputSpecFzOutput file for FixTopology)rDrGN)r_r`rar r9r:r:r:r;r srcs@eZdZdZdZeZeZfddZ fddZ ddZ Z S) FixTopologya This program computes a mapping from the unit sphere onto the surface of the cortex from a previously generated approximation of the cortical surface, thus guaranteeing a topologically correct surface. Examples ======== >>> from nipype.interfaces.freesurfer import FixTopology >>> ft = FixTopology() >>> ft.inputs.in_orig = 'lh.orig' # doctest: +SKIP >>> ft.inputs.in_inflated = 'lh.inflated' # doctest: +SKIP >>> ft.inputs.sphere = 'lh.qsphere.nofix' # doctest: +SKIP >>> ft.inputs.hemisphere = 'lh' >>> ft.inputs.subject_id = '10335' >>> ft.inputs.mgz = True >>> ft.inputs.ga = True >>> ft.cmdline # doctest: +SKIP 'mris_fix_topology -ga -mgz -sphere qsphere.nofix 10335 lh' Zmris_fix_topologyc s|jjrtj|j_d|kr(|jj|d<|jj}t||jjddt||jjddj |d|j_t||jj ddj |dt||jj dddt||jj dd dt t|jf|S) Nr*surf)r7z{0}.orig)r7r.z {0}.inflatedmriz brain.mgzzwm.mgz)r)rr+r,r*rr<rrrrrrrrrun)rr)rd)rr:r;r s&  zFixTopology.runcs>|dkr*tjj|jddd}|j|Stt|j|||S)Nrrr)r+r-r.r$rFrrr)rrrrr)rr:r;r s zFixTopology._format_argcCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r)rr@r:r:r;r s zFixTopology._list_outputs) r_r`rarrrrrrrrrrr:r:)rr;r s  rc@seZdZeddddddZdS)EulerNumberInputSpecz%srTzInput file for EulerNumber)rFrrErDrGNr)r_r`rar r6r:r:r:r;r s rc@s$eZdZejddZejddZdS)EulerNumberOutputSpeczjEuler number of cortical surface. A value of 2 signals a topologically correct surface model with no holes)rGzNumber of defectsN)r_r`rar roeulerdefectsr:r:r:r;r" srcs<eZdZdZdZeZeZfddZ ddZ ddZ Z S) EulerNumbera This program computes EulerNumber for a cortical surface Examples ======== >>> from nipype.interfaces.freesurfer import EulerNumber >>> ft = EulerNumber() >>> ft.inputs.in_file = 'lh.pial' >>> ft.cmdline 'mris_euler_number lh.pial' Zmris_euler_numbercs tj|}|j|j|j|S)N)rr _parse_outputr"r)rr)rr:r;r; s zEulerNumber._run_interfacecCs2tjd|p |}|dkr tdt|j|_dS)z)Parse stdout / stderr and extract defectsz(?<=total defect index = )\d+NzCould not fetch defect index)rrrrr_defects)rr"rrr:r:r;r@ szEulerNumber._parse_outputcCs,|jj}|j|d<dd|j|d<|S)Nrrr)rrr)rr@r:r:r;rG s  zEulerNumber._list_outputs) r_r`rarrrrrrrrrrr:r:)rr;r* s  rc @s:eZdZedd dddddZedd ddgdddd d Zd S)RemoveIntersectionInputSpecz%srTz!Input file for RemoveIntersection)rFrrErDrrGrFr6z"Output file for RemoveIntersection)rFrrDrrrrrGNrr)r_r`rar r6r9r:r:r:r;rN s rc@seZdZedddZdS)RemoveIntersectionOutputSpecFz"Output file for RemoveIntersection)rDrGN)r_r`rar r9r:r:r:r;rc src@s$eZdZdZdZeZeZddZ dS)RemoveIntersectiona) This program removes the intersection of the given MRI Examples ======== >>> from nipype.interfaces.freesurfer import RemoveIntersection >>> ri = RemoveIntersection() >>> ri.inputs.in_file = 'lh.pial' >>> ri.cmdline 'mris_remove_intersection lh.pial lh.pial' Zmris_remove_intersectioncCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;rx s z RemoveIntersection._list_outputsN) r_r`rarrrrrrrr:r:r:r;rg s  rc@s<eZdZejddd6ddddZejddd7ddd d Zeddd d dZ eddddZ eddddZ edddZ eddgddZ eddddZedddgddZejddd Zejd!dd Zejd"d#d Zed$dd%dZed&dd'dZejd(d)d Zejd*dgd)d+Zejd,d-d Zejd.d-d Zejd/d0d Zejd9d4Zd5S):MakeSurfacesInputSpecrHrIrz%sTzHemisphere being processed)rrFrErGr(rzSubject being processed)rrrFrErGz-orig %sz%Implicit input file .orig)rDrErFrGzImplicit input file wm.mgz)rDrErGzImplicit input file filled.mgzz%Implicit input that is sometimes used)rDrGnoaparcz-Implicit input label/.aparc.annot)rDrMrGz-orig_white %sz%Specify a white surface to start with)rFrDrGz -orig_pial %sin_labelz$Specify a pial surface to start with)rFrDrNrGz-fix_mtlzUndocumented flag)rFrGz-nowhitez -whiteonlyzUndocumented flagez-aseg %szInput segmentation filez-T1 %szInput brain or T1 filez-mgzzGNo documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.eduz-noaparc)rFrMrGz -max %.1fz3No documentation (used for longitudinal processing)z-longz -white %szWhite surface namez'If running as a node, set this to True.z+This will copy the input files to the node z directory.)rGNrrzRIf running as a node, set this to True.This will copy the input files to the node z\If running as a node, set this to True.This will copy the input files to the node directory.)r_r`rar rcrrer(r rrrCin_whiter orig_white orig_pialrhZfix_mtlno_whiteZ white_onlyin_asegin_T1rrrjmaximumZ longitudinalrrr:r:r:r;r~ sl   rc@sTeZdZedddZedddZedddZedddZedddZedddZ d S) MakeSurfacesOutputSpecFz&Output white matter hemisphere surface)rDrGz!Output curv file for MakeSurfacesz!Output area file for MakeSurfacesz#Output cortex file for MakeSurfacesz$Output pial surface for MakeSurfacesz&Output thickness file for MakeSurfacesN) r_r`rar out_whiteout_curvout_area out_cortexout_pial out_thicknessr:r:r:r;r s      rcs@eZdZdZdZeZeZfddZ fddZ ddZ Z S) MakeSurfacesa This program positions the tessellation of the cortical surface at the white matter surface, then the gray matter surface and generate surface files for these surfaces as well as a 'curvature' file for the cortical thickness, and a surface file which approximates layer IV of the cortical sheet. Examples ======== >>> from nipype.interfaces.freesurfer import MakeSurfaces >>> makesurfaces = MakeSurfaces() >>> makesurfaces.inputs.hemisphere = 'lh' >>> makesurfaces.inputs.subject_id = '10335' >>> makesurfaces.inputs.in_orig = 'lh.pial' >>> makesurfaces.inputs.in_wm = 'wm.mgz' >>> makesurfaces.inputs.in_filled = 'norm.mgz' >>> makesurfaces.inputs.in_label = 'aparc+aseg.nii' >>> makesurfaces.inputs.in_T1 = 'T1.mgz' >>> makesurfaces.inputs.orig_pial = 'lh.pial' >>> makesurfaces.cmdline 'mris_make_surfaces -T1 T1.mgz -orig pial -orig_pial pial 10335 lh' Zmris_make_surfacesc s|jjr tj|j_d|kr*|jj|d<t||jjdddt||jjdddt||jjddj |jj x&|jj |jj gD]}t||ddqWx,|jj |jj|jjgD]}t||ddqWt|jjrt||jjd d j |jj ntjtjj|jj|jjd tt|jf|S) Nr*rzwm.mgz)r7r.z filled.mgzrz {0}.white)r7rEz{0}.aparc.annot)r)rr+r,r*r<rrCrrrrrrrrr rr1r-r/r(rrr)rr)Z originalfile)rr:r;r s:    zMakeSurfaces.runcs|d krHtjj|}|jjr.tjj|d}n|}|dkr>dS|j|S|d krttjj|}|jdd}|j|S|d kr|jd s|jd rdStjj|}|jdd}|j|St t |j |||S)Nrrrasegrrrrrzlh.origzrh.orig)rr)rr) r+r-r.r)rsplitextrFr$rrrr)rrrrr.rr)rr:r;r s&      zMakeSurfaces._format_argcCs8|jj}tjj|jj|jjd}tjj|jj|jjd}|jjsbtjj|t |jj d|d<tjj|t |jj d|d<tjj|t |jj d|d<t |jj s|jj d kr|dd |d<|dd |d<tjj|t |jj d |d <tjj|t |jj d |d <ntjj|t |jj d|d<|S)NrrEz.whiterz.curvrz.arearZNOWRITEz.pialrz .thicknessrz .cortex.labelr)rrr+r-r/r)r*r(rr?rr rr)rr@dest_dirZ label_dirr:r:r;r/ s, zMakeSurfaces._list_outputs) r_r`rarrrrrrrrrrr:r:)rr;r s & rc@szeZdZedddddddZejdddZejd d dZ ej d d dZ ejd ddZ ej ej ej dddZejddZdS)CurvatureInputSpecz%srTzInput file for Curvature)rFrrErDrrGz -thresh %.3fzUndocumented input threshold)rFrGz-nzUndocumented boolean flagz-a %dzIPerform this number iterative averages of curvature measure before savingz-wzKSave curvature files (will only generate screen output without this option)z-distances %d %dz$Undocumented input integer distancesz$Copy input file to current directory)rGNr)r_r`rar r6r rjrqrhnroZaveragessaveriZ distances copy_inputr:r:r:r;rY s*rc@s$eZdZedddZedddZdS)CurvatureOutputSpecFzMean curvature output file)rDrGzGaussian curvature output fileN)r_r`rar out_mean out_gaussr:r:r:r;rv s rcs4eZdZdZdZeZeZfddZ ddZ Z S) Curvaturea This program will compute the second fundamental form of a cortical surface. It will create two new files ..H and ..K with the mean and Gaussian curvature respectively. Examples ======== >>> from nipype.interfaces.freesurfer import Curvature >>> curv = Curvature() >>> curv.inputs.in_file = 'lh.pial' >>> curv.inputs.save = True >>> curv.cmdline 'mris_curvature -w lh.pial' Zmris_curvaturecs:|jjr&|dkr&tjj|}|j|Stt|j|||S)Nr6) r)rr+r-r.rFrrr)rrrrr.)rr:r;r s   zCurvature._format_argcCsZ|jj}|jjr&tjj|jj}n|jj}tjj|d|d<tjj|d|d<|S)Nz.Hrz.Kr) rrr)rr+r-r.r6r)rr@r6r:r:r;r s zCurvature._list_outputs) r_r`rarrrrrrrrrr:r:)rr;r{ s  rc@seZdZeddddZedd%ddddZedd&ddddZejd d d'ddd dZ ej ddd(ddddZ edddgddddZ ej dddZej dddZej dddZej d*d#Zd$S)+CurvatureStatsInputSpecz-F %sTz'Specify surface file for CurvatureStats)rFrDrGz%srzInput file for CurvatureStats)rFrrErDrGrrHrIrzHemisphere being processed)rrFrErGr(rzSubject being processed)rrrFrErGz-o %sFrz %s.curv.statszOutput curvature stats file)rFrDrrrrGz-mz9Output min / max information for the processed curvature.)rFrGz-Gz-Triggers a series of derived curvature valuesz--writeCurvatureFileszWrite curvature filesz'If running as a node, set this to True.z+This will copy the input files to the node z directory.)rGNrrrrDzRIf running as a node, set this to True.This will copy the input files to the node z\If running as a node, set this to True.This will copy the input files to the node directory.)r_r`rar rf curvfile1 curvfile2r rcrrer(r9rhZmin_maxr>rrr:r:r:r;r sT   rc@seZdZedddZdS)CurvatureStatsOutputSpecFzOutput curvature stats file)rDrGN)r_r`rar r9r:r:r:r;r srcs@eZdZdZdZeZeZfddZ ddZ fddZ Z S) CurvatureStatsa In its simplest usage, 'mris_curvature_stats' will compute a set of statistics on its input . These statistics are the mean and standard deviation of the particular curvature on the surface, as well as the results from several surface-based integrals. Additionally, 'mris_curvature_stats' can report the max/min curvature values, and compute a simple histogram based on all curvature values. Curvatures can also be normalised and constrained to a given range before computation. Principal curvature (K, H, k1 and k2) calculations on a surface structure can also be performed, as well as several functions derived from k1 and k2. Finally, all output to the console, as well as any new curvatures that result from the above calculations can be saved to a series of text and binary-curvature files. Examples ======== >>> from nipype.interfaces.freesurfer import CurvatureStats >>> curvstats = CurvatureStats() >>> curvstats.inputs.hemisphere = 'lh' >>> curvstats.inputs.curvfile1 = 'lh.pial' >>> curvstats.inputs.curvfile2 = 'lh.pial' >>> curvstats.inputs.surface = 'lh.pial' >>> curvstats.inputs.out_file = 'lh.curv.stats' >>> curvstats.inputs.values = True >>> curvstats.inputs.min_max = True >>> curvstats.inputs.write = True >>> curvstats.cmdline 'mris_curvature_stats -m -o lh.curv.stats -F pial -G --writeCurvatureFiles subject_id lh pial pial' Zmris_curvature_statscs<|dkr(tjj|jdd}|j|Stt|j|||S)Nrfrrrr)rfrr)r+r-r.r$rFrrr)rrrrr)rr:r;r s zCurvatureStats._format_argcCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;r s zCurvatureStats._list_outputsc sj|jjrXtj|j_d|kr(|jj|d<t||jjdt||jjdt||jjdt t |j f|S)Nr*r) r)rr+r,r*r<rfrrrrr)rr))rr:r;r s  zCurvatureStats.run) r_r`rarrrrrrrrrrr:r:)rr;r s% rc @sJeZdZeddddddZeddddddZedddd gdd dd d ZdS)JacobianInputSpecz%srTzOriginal surface)rFrrErDrGrzMapped surfaceFr in_origsurfz %s.jacobianz&Output Jacobian of the surface mapping)rFrDrrrrrrGNrrr)r_r`rar rZ in_mappedsurfr9r:r:r:r;r src@seZdZedddZdS)JacobianOutputSpecFz&Output Jacobian of the surface mapping)rDrGN)r_r`rar r9r:r:r:r;r4 src@s$eZdZdZdZeZeZddZ dS)Jacobiana` This program computes the Jacobian of a surface mapping. Examples ======== >>> from nipype.interfaces.freesurfer import Jacobian >>> jacobian = Jacobian() >>> jacobian.inputs.in_origsurf = 'lh.pial' >>> jacobian.inputs.in_mappedsurf = 'lh.pial' >>> jacobian.cmdline 'mris_jacobian lh.pial lh.pial lh.jacobian' Z mris_jacobiancCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;rJ s zJacobian._list_outputsN) r_r`rarrrrrrrr:r:r:r;r8 s  rc@seZdZeddddddZejdddddZed dd d Zedddd dgddZ ej ddddgddZ ej dddd gddZ dS)MRIsCalcInputSpecz%srTz Input file 1)rFrrErDrGrz"Action to perform on input file(s))rFrrErGz-o %szOutput file after calculation)rFrErGrin_floatin_intz Input file 2)rFrDrrMrGz%fin_file2z Input float)rFrrMrGz%dz Input integerNrrrrr)r_r`rar Zin_file1r reactionr9rrjrrorr:r:r:r;rP s& rc@seZdZedddZdS)MRIsCalcOutputSpecFzOutput file after calculation)rDrGN)r_r`rar r9r:r:r:r;ro src@s$eZdZdZdZeZeZddZ dS)MRIsCalca 'mris_calc' is a simple calculator that operates on FreeSurfer curvatures and volumes. In most cases, the calculator functions with three arguments: two inputs and an linking them. Some actions, however, operate with only one input . In all cases, the first input is the name of a FreeSurfer curvature overlay (e.g. rh.curv) or volume file (e.g. orig.mgz). For two inputs, the calculator first assumes that the second input is a file. If, however, this second input file doesn't exist, the calculator assumes it refers to a float number, which is then processed according to .Note: and should typically be generated on the same subject. Examples ======== >>> from nipype.interfaces.freesurfer import MRIsCalc >>> example = MRIsCalc() >>> example.inputs.in_file1 = 'lh.area' # doctest: +SKIP >>> example.inputs.in_file2 = 'lh.area.pial' # doctest: +SKIP >>> example.inputs.action = 'add' >>> example.inputs.out_file = 'area.mid' >>> example.cmdline # doctest: +SKIP 'mris_calc -o lh.area.mid lh.area add lh.area.pial' Z mris_calccCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;r s zMRIsCalc._list_outputsN) r_r`rarrrrrrrr:r:r:r;rs s rc@seZdZejddddZejddddZejddddZejd dd dZe ddd d Z e ddd d Z e dddd Z e dddd Z e ddgd&dZejddd'ddddZe dddgddZejdd(d Zejd*d$Zd%S)+VolumeMaskInputSpecz--label_left_white %dTzLeft white matter label)rFrErGz--label_left_ribbon %dzLeft cortical ribbon labelz--label_right_white %dzRight white matter labelz--label_right_ribbon %dzRight cortical ribbon labelz Implicit input left pial surface)rErDrGz!Implicit input right pial surfacez(Implicit input left white matter surfacez)Implicit input right white matter surfacerz Implicit aseg.mgz segmentation. z6Specify a different aseg by using the 'in_aseg' input.)rDrMrGr(rz%szSubject being processed)rrrFrErGz--aseg_name %srzInput aseg file for VolumeMask)rFrDrMrGz --save_ribbonz'option to save just the ribbon for the z'hemispheres in the format ?h.ribbon.mgz)rFrGz'If running as a node, set this to True.z/This will copy the implicit input files to the znode directory.)rGNzVImplicit aseg.mgz segmentation. Specify a different aseg by using the 'in_aseg' input.rzNoption to save just the ribbon for the hemispheres in the format ?h.ribbon.mgzzVIf running as a node, set this to True.This will copy the implicit input files to the zeIf running as a node, set this to True.This will copy the implicit input files to the node directory.)r_r`rar roZleft_whitelabelZleft_ribbonlabelZright_whitelabelZright_ribbonlabelr lh_pialrh_piallh_whiterh_whiterrer(rrh save_ribbonrr:r:r:r;r sT     rc@s0eZdZedddZedddZedddZdS)VolumeMaskOutputSpecFzOutput cortical ribbon mask)rDrGz Output left cortical ribbon maskz!Output right cortical ribbon maskN)r_r`rar out_ribbon lh_ribbon rh_ribbonr:r:r:r;r s  rcs@eZdZdZdZeZeZfddZ fddZ ddZ Z S) VolumeMaskaH Computes a volume mask, at the same resolution as the /mri/brain.mgz. The volume mask contains 4 values: LH_WM (default 10), LH_GM (default 100), RH_WM (default 20), RH_GM (default 200). The algorithm uses the 4 surfaces situated in /surf/ [lh|rh].[white|pial] and labels voxels based on the signed-distance function from the surface. Examples ======== >>> from nipype.interfaces.freesurfer import VolumeMask >>> volmask = VolumeMask() >>> volmask.inputs.left_whitelabel = 2 >>> volmask.inputs.left_ribbonlabel = 3 >>> volmask.inputs.right_whitelabel = 41 >>> volmask.inputs.right_ribbonlabel = 42 >>> volmask.inputs.lh_pial = 'lh.pial' >>> volmask.inputs.rh_pial = 'lh.pial' >>> volmask.inputs.lh_white = 'lh.pial' >>> volmask.inputs.rh_white = 'lh.pial' >>> volmask.inputs.subject_id = '10335' >>> volmask.inputs.save_ribbon = True >>> volmask.cmdline 'mris_volmask --label_left_ribbon 3 --label_left_white 2 --label_right_ribbon 42 --label_right_white 41 --save_ribbon 10335' Z mris_volmaskc s|jjrtj|j_d|kr(|jj|d<t||jjddt||jjddt||jjddt||jj ddt||jj dt||jj ddt t |jf|S) Nr*rzlh.pialzrh.pialzlh.whitezrh.whiterzaseg.mgz)r)rr+r,r*r<rrrrrrrrr)rr))rr:r;r s  zVolumeMask.runcs4|dkr |jtjj|jdStt|j|||S)Nrz.mgz)rFr+r-r.rstriprrr)rrrr)rr:r;r szVolumeMask._format_argcCsf|jj}tjj|jj|jjd}tjj|d|d<|jjrbtjj|d|d<tjj|d|d<|S)Nrz ribbon.mgzrz rh.ribbon.mgzrz lh.ribbon.mgzr) rrr+r-r/r)r*r(r)rr@r8r:r:r;r s zVolumeMask._list_outputs) r_r`rarrrrrrrrrrr:r:)rr;r s  rc@sveZdZejddd=ddddZejddd>ddd d Zeddd d Z edddd Z edddd Z edddd Z edddd Z edddd Zedddd Zedddd Zedddd Zedddd ZedddZejd?dddZejdddZeddd d!Zed"dd#gd$d%Zed&dd'd(gd)d%Zejd*d+dZed,d-dd.gd/d0Zed1d-dd#gd2d3ZejdAd7Zejd8d9gd:d;Zd/mri/wm.mgz)rErDrGz-Input file must be /surf/lh.whitez-Input file must be /surf/rh.whitez,Input file must be /surf/lh.pialz,Input file must be /surf/rh.pialz/mri/transforms/talairach.xfmz1Input file must be /surf/?h.thicknessz1Input file must be /mri/brainmask.mgzz4Input file must be /mri/aseg.presurf.mgzz.Input file must be /mri/ribbon.mgzz'implicit input file {hemi}.cortex.label)rDrGrzInput surface (e.g. 'white'))rrFrGz-mgzzLook for mgz files)rFrGz -cortex %szInput cortex label)rFrDrGz-a %srzCcompute properties for each label in the annotation file separately)rFrDrMrGz-l %sZ in_annotatoin out_colorz%limit calculations to specified labelz-bzTabular outputz-f %sFtabular_outputzTable output to tablefile)rFrDr^rNrGz-c %sz1Output annotation files's colortable to text file)rFrDr^rMrGz'If running as a node, set this to True.z+This will copy the input files to the node z directory.)rGz-th3 cortex_labelz8turns on new vertex-wise volume calc for mris_anat_stats)rFrNrGNrrrzRIf running as a node, set this to True.This will copy the input files to the node z\If running as a node, set this to True.This will copy the input files to the node directory.)r_r`rar rer(rcrr rArrrrrjr brainmaskrribbonrrfrhrZ in_cortex in_annotationrr out_tablerrZth3r:r:r:r;r s     rc@s$eZdZedddZedddZdS)ParcellationStatsOutputSpecFzTable output to tablefile)rDrGz1Output annotation files's colortable to text fileN)r_r`rar rrr:r:r:r;r s rcs<eZdZdZdZeZeZfddZ ddZ ddZ Z S) ParcellationStatsa This program computes a number of anatomical properties. Examples ======== >>> from nipype.interfaces.freesurfer import ParcellationStats >>> import os >>> parcstats = ParcellationStats() >>> parcstats.inputs.subject_id = '10335' >>> parcstats.inputs.hemisphere = 'lh' >>> parcstats.inputs.wm = './../mri/wm.mgz' # doctest: +SKIP >>> parcstats.inputs.transform = './../mri/transforms/talairach.xfm' # doctest: +SKIP >>> parcstats.inputs.brainmask = './../mri/brainmask.mgz' # doctest: +SKIP >>> parcstats.inputs.aseg = './../mri/aseg.presurf.mgz' # doctest: +SKIP >>> parcstats.inputs.ribbon = './../mri/ribbon.mgz' # doctest: +SKIP >>> parcstats.inputs.lh_pial = 'lh.pial' # doctest: +SKIP >>> parcstats.inputs.rh_pial = 'lh.pial' # doctest: +SKIP >>> parcstats.inputs.lh_white = 'lh.white' # doctest: +SKIP >>> parcstats.inputs.rh_white = 'rh.white' # doctest: +SKIP >>> parcstats.inputs.thickness = 'lh.thickness' # doctest: +SKIP >>> parcstats.inputs.surface = 'white' >>> parcstats.inputs.out_table = 'lh.test.stats' >>> parcstats.inputs.out_color = 'test.ctab' >>> parcstats.cmdline # doctest: +SKIP 'mris_anatomical_stats -c test.ctab -f lh.test.stats 10335 lh white' Zmris_anatomical_statsc s:|jjrtj|j_d|kr*|jj|d<t||jjddt||jjddt||jjddt||jj ddt||jj ddt||jj tj j dd d t||jjdd t||jjdd t||jjdd t||jjddj|jjt|jjrt||jjddj|jjt|jtt|jf|S)Nr*rzlh.whitezlh.pialzrh.whitezrh.pialrzwm.mgzZ transformsz talairach.xfmz brainmask.mgzzaseg.presurf.mgzz ribbon.mgzz {0}.thicknessrEz{0}.cortex.label)r)rr+r,r*r<rrrrrArjr-r/rrrrrrr rrBrrrr)rr))rr:r;r s<     zParcellationStats.runcCs|dkr|j|SdS)Nrr)rr)r)rrr:r:r;r s zParcellationStats._gen_filenamecCs|jj}t|jjr.tjj|jj|d<ntjj|jj |jj d}t|jj r|jj dkrxtjj |jj jdd}qtjj |jj jdd}n\t|jjr|jj dkrtjj |jjjdd}qtjj |jjjdd}nt|jjd}tjj|||d<t|jjr$tjj|jj|d <ntjj|jj |jj d }t|jj rtjj |jj }xdD]}|j|d}q`W|}d|krtjj||d|d <ntjj|d|d|d <ntjj|d|d <|S)Nrstatsrz.annotz .pial.statsz.statsz.labelz.aparc.annot.statsrrElh.rh.aparc.annotryZBAZctabz aparc.annot.zaparc.annot.ctab)rrrr)rrr r)rr+r-rr/r*r(rrfr.replacerr?rr)rr@Z stats_dirr.r8itemrr:r:r;r sD            zParcellationStats._list_outputs) r_r`rarrrrrrrrrrr:r:)rr;r s #rc@seZdZejddddddZejddddd d Zeddd d Z eddd d Z edddd Z edddd Z eddddZ eddddZejddZdS)ContrastInputSpecr(z--s %sTzSubject being processed)rFrrErGrHrIz --%s-onlyzHemisphere being processed)rFrErGz1Input file must be /surf/?h.thickness)rErDrGz7Input file must be /surf/.whitezIInput annotation file must be /label/.aparc.annotzGInput cortex label must be /label/.cortex.labelz Implicit input file mri/orig.mgz)rDrErGz"Implicit input file mri/rawavg.mgzz'If running as a node, set this to True.z+This will copy the input files to the node z directory.)rGNzRIf running as a node, set this to True.This will copy the input files to the node z\If running as a node, set this to True.This will copy the input files to the node directory.)r_r`rar rer(rcrr rr annotationrrrawavgrhrr:r:r:r;r sB rc@s0eZdZedddZedddZedddZdS)ContrastOutputSpecFz"Output contrast file from Contrast)rDrGzOutput stats file from ContrastTzOutput log from ContrastN)r_r`rar out_contrast out_statsrwr:r:r:r;r=s  rcs4eZdZdZdZeZeZfddZ ddZ Z S)Contrasta Compute surface-wise gray/white contrast Examples ======== >>> from nipype.interfaces.freesurfer import Contrast >>> contrast = Contrast() >>> contrast.inputs.subject_id = '10335' >>> contrast.inputs.hemisphere = 'lh' >>> contrast.inputs.white = 'lh.white' # doctest: +SKIP >>> contrast.inputs.thickness = 'lh.thickness' # doctest: +SKIP >>> contrast.inputs.annotation = '../label/lh.aparc.annot' # doctest: +SKIP >>> contrast.inputs.cortex = '../label/lh.cortex.label' # doctest: +SKIP >>> contrast.inputs.rawavg = '../mri/rawavg.mgz' # doctest: +SKIP >>> contrast.inputs.orig = '../mri/orig.mgz' # doctest: +SKIP >>> contrast.cmdline # doctest: +SKIP 'pctsurfcon --lh-only --s 10335' Z pctsurfconc s|jjrtj|j_d|kr(|jj|d<|jj}t||jjddj|t||jj ddj|t||jj ddj|t||jj ddj|t||jj dd t||jj dd t|jtt|jf|S) Nr*rEz{0}.aparc.annotz{0}.cortex.labelrz {0}.whitez {0}.thicknessrzorig.mgzz rawavg.mgz)r)rr+r,r*rr<rrrrrrrrBrrrr)rr)rd)rr:r;r[s    z Contrast.runcCsz|jj}tjj|jj|jj}tjj|dt|jj d|d<tjj|dt|jj d|d<tjj|dd|d <|S) Nrz .w-g.pct.mghrrz.w-g.pct.statsrscriptszpctsurfcon.logrw) rrr+r-r/r)r*r(r?r)rr@Z subject_dirr:r:r;rqs zContrast._list_outputs) r_r`rarrrrrrrrrr:r:)rr;rCs  rc @sleZdZedddddZedddddZeddddddZed ddddd d ZeddddgdddddZ dS)RelabelHypointensitiesInputSpecTz$Implicit input file must be lh.white)rErDrrGz$Implicit input file must be rh.whitez%srzInput aseg file)rFrrErDrGrrz*Directory containing lh.white and rh.white)rFrrDrrGrFrz %s.hypos.mgzzOutput aseg file)rFrrDrrrrrGNrrr) r_r`rar rrrrZsurf_directoryr9r:r:r:r;r~s8rc@seZdZeddddZdS) RelabelHypointensitiesOutputSpecz%sFzOutput aseg file)rFrDrGN)r_r`rar r9r:r:r:r;rsrc@s$eZdZdZdZeZeZddZ dS)RelabelHypointensitiesa Relabel Hypointensities Examples ======== >>> from nipype.interfaces.freesurfer import RelabelHypointensities >>> relabelhypos = RelabelHypointensities() >>> relabelhypos.inputs.lh_white = 'lh.pial' >>> relabelhypos.inputs.rh_white = 'lh.pial' >>> relabelhypos.inputs.surf_directory = '.' >>> relabelhypos.inputs.aseg = 'aseg.mgz' >>> relabelhypos.cmdline 'mri_relabel_hypointensities aseg.mgz . aseg.hypos.mgz' Zmri_relabel_hypointensitiescCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;rs z$RelabelHypointensities._list_outputsN) r_r`rarrrrrrrr:r:r:r;rs rc@s(eZdZejddddddZeddddd Zeddd d Zeddd d Z eddd d Z edddd Z edddd Z edddd Z edddd Zedddd Zedddd ZedddZeddddZejdddZeddddZejdddZejd d!dZejd"d#dZejd$d%dZejd&d'Zd(S))Aparc2AsegInputSpecr(z--s %sTzSubject being processed)rFrrErGz--o %sFz4Full path of file to save the output segmentation in)rFrDrErGz-Input file must be /surf/lh.white)rErDrGz-Input file must be /surf/rh.whitez,Input file must be /surf/lh.pialz,Input file must be /surf/rh.pialz1Input file must be /mri/lh.ribbon.mgzz1Input file must be /mri/rh.ribbon.mgzz.Input file must be /mri/ribbon.mgzz4Input file must be /label/lh.aparc.annotz4Input file must be /label/rh.aparc.annotz7Implicit input filled file. Only required with FS v5.3.)rDrGz --aseg %szInput aseg file)rFrDrGz --volmaskzVolume mask flag)rFrGz --ctxseg %sryz --labelwmzFor each voxel labeled as white matter in the aseg, re-assign its label to be that of the closest cortical point if its distance is less than dmaxctx.z --hypo-as-wmzLabel hypointensities as WMz --rip-unknownz0Do not label WM based on 'unknown' corical labelz--a2009szUsing the a2009s atlasz\If running as a node, set this to True.This will copy the input files to the node directory.)rGN)r_r`rar rer(r r9rrrrrrr lh_annotation rh_annotationfilledrrhZvolmaskZctxsegZlabel_wmZhypo_wmZ rip_unknownZa2009srr:r:r:r;rsr    rc@seZdZedddZdS)Aparc2AsegOutputSpecz%szOutput aseg file)rFrGN)r_r`rar r9r:r:r:r;rsrcs@eZdZdZdZeZeZfddZ fddZ ddZ Z S) Aparc2Asega Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. The algorithm is to find each aseg voxel labeled as cortex (3 and 42) and assign it the label of the closest cortical vertex. If the voxel is not in the ribbon (as defined by mri/ lh.ribbon and rh.ribbon), then the voxel is marked as unknown (0). This can be turned off with ``--noribbon``. The cortical parcellation is obtained from subject/label/hemi.aparc.annot which should be based on the curvature.buckner40.filled.desikan_killiany.gcs atlas. The aseg is obtained from subject/mri/aseg.mgz and should be based on the RB40_talairach_2005-07-20.gca atlas. If these atlases are used, then the segmentations can be viewed with tkmedit and the FreeSurferColorLUT.txt color table found in ``$FREESURFER_HOME``. These are the default atlases used by ``recon-all``. Examples -------- >>> from nipype.interfaces.freesurfer import Aparc2Aseg >>> aparc2aseg = Aparc2Aseg() >>> aparc2aseg.inputs.lh_white = 'lh.pial' >>> aparc2aseg.inputs.rh_white = 'lh.pial' >>> aparc2aseg.inputs.lh_pial = 'lh.pial' >>> aparc2aseg.inputs.rh_pial = 'lh.pial' >>> aparc2aseg.inputs.lh_ribbon = 'label.mgz' >>> aparc2aseg.inputs.rh_ribbon = 'label.mgz' >>> aparc2aseg.inputs.ribbon = 'label.mgz' >>> aparc2aseg.inputs.lh_annotation = 'lh.pial' >>> aparc2aseg.inputs.rh_annotation = 'lh.pial' >>> aparc2aseg.inputs.out_file = 'aparc+aseg.mgz' >>> aparc2aseg.inputs.label_wm = True >>> aparc2aseg.inputs.rip_unknown = True >>> aparc2aseg.cmdline # doctest: +SKIP 'mri_aparc2aseg --labelwm --o aparc+aseg.mgz --rip-unknown --s subject_id' Zmri_aparc2asegc s|jjrtj|j_d|kr(|jj|d<t||jjddt||jjddt||jjddt||jj ddt||jj ddt||jj dd t||jj dd t||jj dt||jjdd t||jjd t||jjd tt|jf|S) Nr*rzlh.whitezlh.pialzrh.whitezrh.pialrz lh.ribbon.mgzz rh.ribbon.mgzz ribbon.mgzz filled.mgzrE)r)rr+r,r*r<rrrrrrrrrrrrrr)rr))rr:r;rBs   zAparc2Aseg.runcsT|dkr&tjj|jdd}|j|S|dkr@|jtjj|Stt|j|||S)Nrz.mgzryr9) r+r-r.rrFrrrr)rrrrr.)rr:r;rUs  zAparc2Aseg._format_argcCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;r_s zAparc2Aseg._list_outputs) r_r`rarrrrrrrrrrr:r:)rr;rs$  rc@s*eZdZedddddZeddddZdS) Apas2AsegInputSpecz--i %sTzInput aparc+aseg.mgz)rFrErDrGz--o %szOutput aseg file)rFrErGN)r_r`rar r6r9r:r:r:r;resrc@seZdZeddddZdS)Apas2AsegOutputSpecz%sFzOutput aseg file)rFrDrGN)r_r`rar r9r:r:r:r;rmsrc@s$eZdZdZdZeZeZddZ dS) Apas2Asega3 Converts aparc+aseg.mgz into something like aseg.mgz by replacing the cortical segmentations 1000-1035 with 3 and 2000-2035 with 42. The advantage of this output is that the cortical label conforms to the actual surface (this is not the case with aseg.mgz). Examples -------- >>> from nipype.interfaces.freesurfer import Apas2Aseg >>> apas2aseg = Apas2Aseg() >>> apas2aseg.inputs.in_file = 'aseg.mgz' >>> apas2aseg.inputs.out_file = 'output.mgz' >>> apas2aseg.cmdline 'apas2aseg --i aseg.mgz --o output.mgz' Z apas2asegcCs$|jj}tjj|jj|d<|S)Nr9)rrr+r-rr)r9)rr@r:r:r;rs zApas2Aseg._list_outputsN) r_r`rarrrrrrrr:r:r:r;rqs rc@seZdZedddd%dddZejddd&d d Zejd dd'dd dZ ej dddZ ejddddZ ejddddZ ejdddddZejdddZejdddZejdddZejd d!dZejd"d#dZd$S)(MRIsExpandInputSpecTz%srFzSurface to expand)rDrErFrrrGz%grz0Distance in mm or fraction of cortical thickness)rErFrrGexpandedrz~Output surface file. If no path, uses directory of ``in_file``. If no path AND missing "lh." or "rh.", derive from ``in_file``)rFrrrGz -thicknessz0Expand by fraction of cortical thickness, not mm)rFrGz-thickness_name %szName of thickness file (implicit: "thickness") If no path, uses directory of ``in_file`` If no path AND missing "lh." or "rh.", derive from `in_file`)rFrrGz-pial %szName of pial file (implicit: "pial") If no path, uses directory of ``in_file`` If no path AND missing "lh." or "rh.", derive from ``in_file``rz!WARNING: Do not change this trait)rrrGz-S %gzSpring term (implicit: 0.05)z-T %gzdt (implicit: 0.25)z-W %dz/Write snapshots of expansion every N iterationsz-A %dz0Smooth surface with N iterations after expansionz-N %dz-Number of surfacces to write during expansionNrrr)r_r`rar r6r rjZdistancermrUrhrthickness_namerrZspringdtroZwrite_iterationsZsmooth_averagesZ nsurfacesr:r:r:r;rsR   rc@seZdZeddZdS)MRIsExpandOutputSpeczOutput surface file)rGN)r_r`rar r9r:r:r:r;rsrc@s,eZdZdZdZeZeZddZ ddZ dS) MRIsExpanda Expands a surface (typically ?h.white) outwards while maintaining smoothness and self-intersection constraints. Examples ======== >>> from nipype.interfaces.freesurfer import MRIsExpand >>> mris_expand = MRIsExpand(thickness=True, distance=0.5) >>> mris_expand.inputs.in_file = 'lh.white' >>> mris_expand.cmdline 'mris_expand -thickness lh.white 0.5 expanded' >>> mris_expand.inputs.out_name = 'graymid' >>> mris_expand.cmdline 'mris_expand -thickness lh.white 0.5 graymid' Z mris_expandcCs(|jj}|j|jj|jj|d<|S)Nr9)rr_associated_filer)r6rU)rr@r:r:r;rs zMRIsExpand._list_outputscCs||jj}|jj}t|sd}|j|||j_t|jjrd|jjrd|jj}t|sTd}|j|||j_|j||jj|j_dS)z Filename normalization routine to perform only when run in Node context. Find full paths for pial, thickness and sphere files for copying. rrN)r)r6rr rrrr)rr6rrr:r:r;r:szMRIsExpand.normalize_filenamesN) r_r`rarrrrrrrr:r:r:r:r;rs rc@s*eZdZd-Zejeddd d ded d Zedd deddZedddeddZ edddeddZ edddeddZ edddeddZ ejej edddZejej edddZejej edddZejej edd dZejej ed!d"dZej d#d$Zej d%d&gd'Zedd(d)Zedd*d)Zej d+d$Zd,S).LTAConvertInputSpecin_ltain_fslin_mniin_reg in_niftyregin_itkT)rDzidentity.nofilez --inlta %szinput transform of LTA type)rFrErMrGz --infsl %szinput transform of FSL type)rDrFrErMrGz --inmni %szinput transform of MNI/XFM typez --inreg %sz2input transform of TK REG type (deprecated format)z--inniftyreg %sz3input transform of Nifty Reg type (inverse RAS2RAS)z --initk %szinput transform of ITK typez --outlta %sz/output linear transform (LTA Freesurfer format))rFrGz --outfsl %szoutput transform in FSL formatz --outmni %sz"output transform in MNI/XFM formatz --outreg %sz"output transform in reg dat formatz --outitk %szoutput transform in ITK formatz--invert)rFz --ltavox2voxout_lta)rFrNz--src %s)rDrFz--trg %sz --trgconformN)r r r r rr)r_r`raZ_in_xorr rlr r r r r rrrhrout_fslout_mniout_regout_itkinvertZ ltavox2voxrbZ target_fileZtarget_conformr:r:r:r;r s|   r c@sHeZdZedddZedddZedddZedddZedddZdS) LTAConvertOutputSpecTz/output linear transform (LTA Freesurfer format))rDrGzoutput transform in FSL formatz"output transform in MNI/XFM formatz"output transform in reg dat formatzoutput transform in ITK formatN) r_r`rar rrrrrr:r:r:r;ras     rcs4eZdZdZeZeZdZfddZ ddZ Z S) LTAConverta:Convert different transformation formats. Some formats may require you to pass an image if the geometry information is missing form the transform file format. For complete details, see the `lta_convert documentation. `_ Z lta_convertcs2|jdr|dkr|j|}tt|j|||S)NZout_T) startswithrrrr)rrrr)rr:r;rvs zLTAConvert._format_argcCsR|jj}x@dD]8\}}t|j|}|r|d kr6|n|}tjj|||<qW|S)Nrout.ltarout.matrout.xfmrout.datrout.txtTrrrrrrrrrr)rrr r!r")rrrr)r+r-r)rr@rrBattrfnamer:r:r;r{s   zLTAConvert._list_outputs) r_r`rarr rrrrrrrr:r:)rr;ris  r)NNN)rr+rr3ryrZutils.filemaniprrrrrr r r r r rrrrrrrrZ __docformat__r|r~rqrr getLoggerrr<rBrCrvrwrrrrrrrrrrrrrrrr r rr'r.r0r4r6r7r;r=r>r@rGrHrIrJrKrLrNrOrRrVrXrYrZr[r\rdrgrirlrmrnrrrsrtrvryrzr|r}rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrr:r:r:r;sV ( $   !. 45f52,d5 5 &6!&62 HM. $ $!,> $I  &9A#<=m0;%SMO2O