3 d@sdZddlZddlmZmZddlmZmZmZm Z m Z m Z m Z ddlm Z mZdd lmZd ZGd d d eZGd ddeZGddde ZGdddeZGdddeZGdddeZGdddeZGddde ZGdddeZGdddeZGdd d eZGd!d"d"e ZGd#d$d$eZGd%d&d&eZGd'd(d(e Z Gd)d*d*eZ!Gd+d,d,eZ"Gd-d.d.e Z#Gd/d0d0e!Z$Gd1d2d2e#Z%Gd3d4d4eZ&Gd5d6d6eZ'Gd7d8d8e Z(Gd9d:d:eZ)Gd;d<dd>e Z+Gd?d@d@eZ,GdAdBdBeZ-GdCdDdDe Z.GdEdFdFeZ/GdGdHdHeZ0GdIdJdJe Z1GdKdLdLeZ2GdMdNdNeZ3GdOdPdPe Z4dS)QzYThe freesurfer module provides basic functions for interfacing with freesurfer tools. N)fname_presuffixsplit_filename) TraitedSpecFiletraitsInputMultiPathOutputMultiPath Directory isdefined) FSCommand FSTraitedSpec) copy2subjdirZrestructuredtextc@sFeZdZeddddZejddddZejdd d dd dZ ejd d9ddZ ejdd:ddZ ej dd;ddZ edddd dZejd!d"d#Zejd$d%d#Zeejeddeddd&d'd#Zejd(d)d#Zejd*d+gd,dZejd-d.gd/dZejd0d1gd2dZejd3d4gd5dZejd6d7d#Zd8S)?MRISPreprocInputSpecz--out %sTzoutput filename)argstrgenfiledescz --target %sztarget subject name)r mandatoryrlhrhz --hemi %sz hemisphere for source and targetz --meas %s surf_measuresurf_measure_file surf_areaz+Use subject/surf/hemi.surf_measure as input)rxorrz --area %szDExtract vertex area from subject/surf/hemi.surfname to use as input.z --s %s...subjects fsgd_file subject_filez)subjects from who measures are calculatedz --fsgd %sz specify subjects using fsgd file)existsrrrz--f %sz1file specifying subjects separated by white space)rz --is %s...z=file alternative to surfmeas, still requires list of subjectsz --srcfmt %sz source format)rrz --surfdir %sz'alternative directory (instead of surf)z --iv %s %s...z*list of volume measure and reg file tuplesz --projfrac %sz projection fraction for vol2surfz --fwhm %f num_itersz'smooth by fwhm mm on the target surfacez --niters %dfwhmz/niters : smooth by niters on the target surfacez --fwhm-src %fnum_iters_sourcez'smooth by fwhm mm on the source surfacez--niterssrc %d fwhm_sourcez/niters : smooth by niters on the source surfacez--smooth-cortex-onlyz,only smooth cortex (ie, exclude medial wall)N)rrr)rrr)rrr)rrr)rrr)rrr)__name__ __module__ __qualname__rout_filerStrtargetEnumhemirrListrrrr rZ source_formatsurf_dirTupleZvol_measure_fileFloatZ proj_fracr!Intr r#r"BoolZsmooth_cortex_onlyr2r2D/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/freesurfer/model.pyrs   rc@seZdZeddZdS)MRISPreprocOutputSpeczpreprocessed output file)rN)r$r%r&rr'r2r2r2r3r4msr4c@s,eZdZdZdZeZeZddZ ddZ dS) MRISPreprocaWUse FreeSurfer mris_preproc to prepare a group of contrasts for a second level analysis Examples -------- >>> preproc = MRISPreproc() >>> preproc.inputs.target = 'fsaverage' >>> preproc.inputs.hemi = 'lh' >>> preproc.inputs.vol_measure_file = [('cont1.nii', 'register.dat'), ('cont1a.nii', 'register.dat')] >>> preproc.inputs.out_file = 'concatenated_file.mgz' >>> preproc.cmdline 'mris_preproc --hemi lh --out concatenated_file.mgz --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat' Z mris_preproccCsN|jj}|jj}||d<t|sJtjjtjd|jj |jj f|d<|S)Nr'zconcat_%s_%s.mgz) output_specgetinputsr'r ospathjoingetcwdr+r))selfoutputsoutfiler2r2r3 _list_outputss  zMRISPreproc._list_outputscCs|dkr|j|SdS)Nr')r@)r=namer2r2r3 _gen_filenames zMRISPreproc._gen_filenameN) r$r%r&__doc___cmdr input_specr4r6r@rBr2r2r2r3r5qs  r5c@sreZdZedddddZeeddd d d gd d ZeddgdZeddgdZe j ddddddZ e j ddZ dS)MRISPreprocReconAllInputSpecTz --meas %srrrzfile necessary for surfmeas)rrrr)rz --surfreg %slh_surfreg_targetrh_surfreg_targetz*lh and rh input surface registration files)rrequiresrz)Implicit target surface registration file surfreg_files)rrI subject_idz--s %srrrz)subject from whom measures are calculated)r usedefaultrrzaIf running as a node, set this to True this will copy some implicit inputs to the node directory.)rN)rrr)rrrrK)r$r%r&rrr rJrGrHrStringrKr1 copy_inputsr2r2r2r3rFs,  rFcs0eZdZdZeZfddZfddZZS)MRISPreprocReconAllaUExtends MRISPreproc to allow it to be used in a recon-all workflow Examples -------- >>> preproc = MRISPreprocReconAll() >>> preproc.inputs.target = 'fsaverage' >>> preproc.inputs.hemi = 'lh' >>> preproc.inputs.vol_measure_file = [('cont1.nii', 'register.dat'), ('cont1a.nii', 'register.dat')] >>> preproc.inputs.out_file = 'concatenated_file.mgz' >>> preproc.cmdline 'mris_preproc --hemi lh --out concatenated_file.mgz --s subject_id --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat' c s|jjrtj|j_d|kr(|jj|d<t|jjr>|jj}nd}t|jjrxj|jjD]^}tjj |}t |||||j drt ||jj |||jj dqXt ||jj|||jj dqXWt|jjrt ||jj|tt|jf|S)N subjects_dirsurfzlh.)rK)r8rNr9r<rPr 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descriptor file)rrrz--X %szdesign matrix file)rrrrz --C %s...z contrast file)rrz--osgmcontrastz,construct X and C as a one-sample group meanz--no-contrasts-okz%do not fail if no contrasts specifiedz --pvr %s...zper-voxel regressorsz--selfreg %d %d %dz'self-regressor from index col row slicez--wls %s weight_file weight_inv weight_sqrtzweighted least squaresz --yffxvar %szfor fixed effects analysis)rrrz --ffxdof %dfixed_fx_dof_filezdof for fixed effects analysisz--ffxdofdat %d fixed_fx_dofz-text file with dof for fixed effects analysis weighted_lsz#weight for each input at each voxel)rrrz--w-invzinvert weights)rrrz--w-sqrtzsqrt of weightsgz --fwhm %fzsmooth input by fwhm)lowrrz --var-fwhm %fzsmooth variance by fwhmz--no-mask-smoothzdo not mask when smoothingz --no-est-fwhmzturn off FWHM output estimationz --mask %sz binary maskz --label %scortexz use label as mask, surfaces onlyz--cortex label_filez%use subjects ?h.cortex.label as labelz --mask-invz invert maskz--prunezCremove voxels 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mask used in the analysisz#text file with estimated smoothnessz>> glmfit = GLMFit() >>> glmfit.inputs.in_file = 'functional.nii' >>> glmfit.inputs.one_sample = True >>> glmfit.cmdline == 'mri_glmfit --glmdir %s --y functional.nii --osgm'%os.getcwd() True Z mri_glmfitcs8|dkr$|j}|j|j|j|jfStt|j|||S)NrQ)r8rrKr+rxrTrrY)r=rArZr[Z_si)rWr2r3rYszGLMFit._format_argcs>|jj}t|jjs"tjntjj|jj|d<tjj d|d<tjj d|d<tjj d|d<tjj d|d <tjj d |d <tjj d |d <t|jj r|jj rtjj d|d<t|jj r|jj rtjj d|d<t|jj rVg}xn|jj D]B}t |dd+kr8|jt |dn|jtjj|dqWnt|jjrt|jjrtdg}fdd|D|d<fdd|D|d<fdd|D|d<fd d|D|d!<t|jjr:|jjr:tjj d"}tjj |d#|d$<tjj |d%|d&<tjj |d'|d(<tjj |d)|d*<|S),Nrqzbeta.mghr~zrvar.mghrzrstd.mghrzmask.mghrtzfwhm.datrzdof.datrzeres.mghrzyhat.mghrr.mat.dat.mtx.conr Zosgmcsg|]}tjj|dqS)zsig.mgh)r9r:r;).0c)glmdirr2r3 sz(GLMFit._list_outputs..rcsg|]}tjj|dqS)zF.mgh)r9r:r;)rr)rr2r3rsrcsg|]}tjj|dqS)z gamma.mgh)r9r:r;)rr)rr2r3rsrcsg|]}tjj|dqS)z gammavar.mgh)r9r:r;)rr)rr2r3rsrzpca-ereszv.mghrzu.mtxrz sdiag.matZsingluar_valuesz stats.datr)rrrr)r6r7r r8rqr9r<r:abspathr;rwrvrbrappendsplitrarz)r=r>Z contrastsrZpcadirr2)rr3r@sD   zGLMFit._list_outputscCs|dkrtjSdS)Nrq)r9r<)r=rAr2r2r3rB szGLMFit._gen_filename) r$r%r&rCrDr]rEr}r6rYr@rBr\r2r2)rWr3rs  5rcseZdZfddZZS)OneSampleTTestc stt|jf|d|j_dS)NT)rTr__init__r8ra)r=kwargs)rWr2r3rszOneSampleTTest.__init__)r$r%r&rr\r2r2)rWr3rsrc@seZdZeddddddZejddgdd Zejd dgd d Zejd d dZ ejdddZ ej ej dddZ ejdddZejdddZejdddgdd ZeddddZejddd d!d"dZejejed#d$dZej d%d&dZej d'd(dZejd)d*dZej d+d,dZedd-d.d/Zedd0d1d/Zejd2d3dZejd4d5dZejd6d7dZejd8d9dZ ejd:d;dZ!ej dd?dZ#ej d@dAdZ$dBS)CBinarizeInputSpecTz--i %sFz input volume)rrrr^rz--min %f wm_ven_csfz min thresh)rrrz--max %fz max threshz --rmin %fz$compute min based on rmin*globalmean)rrz --rmax %fz$compute max based on rmax*globalmeanz --match %d...zmatch instead of thresholdz--wmz1set match vals to 2 and 41 (aseg for cerebral WM)z --ventriclesz:set match vals those for aseg ventricles+choroid (not 4th)z --wm+vcsfrmmaxz3WM and ventricular CSF, including choroid (not 4th)z--o %szbinary output volume)rrrZniiznii.gzZmgzzoutput file typez --count %sz6save number of hits in ascii file (hits, ntotvox, pct)z --binval %dz+set vox within thresh to val (default is 1)z--binvalnot %dz+set vox outside range to val (default is 0)z--invzset binval=0, binvalnot=1z --frame %sz)use 0-based frame of input (default is 0)z --merge %szmerge with mergevol)rrrz--mask maskvolzmust be within maskz--mask-thresh %fzset thresh for maskz--absz+take abs of invol first (ie, make unsigned)z--bincolz.set binarized voxel value to its column numberz --zero-edgeszzero the edge voxelsz--zero-slice-edgeszzero the edge slice voxelsz --dilate %dz!niters: dilate binarization in 3Dz --erode %dz5nerode: erode binarization in 3D (after any dilation)z --erode2d %dz9nerode2d: erode binarization in 2D (after any 3D erosion)N)%r$r%r&rrrrr/rmrZrminZrmaxr,r0matchr1ZwmZ ventriclesr binary_filer*out_typeEither count_fileZbin_valZ bin_val_notinvertZframe_noZ merge_filert 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ejddddddd ddZ ejdddddddddZ ej dddZ ejdd dZejd!d"dZejd#d$dZedd%d&d'Zejd(d)dZejd*d+dZejd,d-dZejd.d/dZedd0d1d'Zejd2d3dZejd4d5dZd6S)7ConcatenateInputSpecT)rz%Individual volumes to be concatenatedz --i %s...)rrrz Output volumez--o %s)rrrrnrorpz--%sz3Take only pos or neg voxles from input, or take abs)rrsumvarZstdrrmZmeanz@Compute the sum, var, std, max, min or mean of the input volumesavgZdiffz diff-normz diff-norm1z diff-norm2z --paired-%sz Compute paired sum, avg, or diffz --gmean %dz0create matrix to average Ng groups, Nper=Ntot/Ngz --mean-div-nz#compute mean/nframes (good for var)z--mul %fz$Multiply input volume by some amountz--add %fz#Add some amount to the input volumez--mtx %sz)Multiply input by an ascii matrix in file)rrrz --combinez0Combine non-zero values into single frame volumez--keep-datatypez/Keep voxelwise precision type (default is floatz --max-bonfcorz7Compute max and bonferroni correct (assumes -log10(ps))z --max-indexz6Compute the index of max voxel in concatenated volumesz --mask %szMask input with a volumez--votez>> concat = Concatenate() >>> concat.inputs.in_files = ['cont1.nii', 'cont2.nii'] >>> concat.inputs.concatenated_file = 'bar.nii' >>> concat.cmdline 'mri_concat --o bar.nii --i cont1.nii --i cont2.nii' Z mri_concatcCs:|jj}|jj}t|s d}tjjtj||d<|S)Nzconcat_output.nii.gzr) r6r7r8rr r9r:r;r<)r=r>rr2r2r3r@s  zConcatenate._list_outputscCs|dkr|j|SdS)Nr)r@)r=rAr2r2r3rB s zConcatenate._gen_filenameN) r$r%r&rCrDrrErr6r@rBr2r2r2r3rs  rc @seZdZdrZeddedddZejejej dd ejd edd d Z ejejej dd ejd eddd Z edddsddZ eddddZ eddddZejdddZejdddZejdddZej dd d!d"dZdtZedd&ed'd(Zejd)ed*d+Zedd,ed-d(Zejd.d/dZejd0d1dZejd2d3dZejd4d5dZejd6d7dZejd8d9dZ ejd:d;dZ!eddd?dZ#ej d@dAdBdCdDdEZ$ejdFdGgdHdIZ%ejdJdKdZ&ejdLdMdZ'ej dNdOd!dPdZ(edQddRdSZ)ejdTdUdZ*ej dVdWdXdYdEZ+ej,ejedZd[dZ-ej,ejed\d]dZ.ej,ejed^d_dZ/ejejd`dadZ0ejdbdcdZ1ejdddedZ2ejdfdgdZ3ejdhdidZ4edjdkdZ5ej dldmdngdodpZ6dqS)uSegStatsInputSpecsegmentation_fileannot surf_labelTz--seg %szsegmentation volume path)rrrrrrrz--annot %s %s %sz,subject hemi parc : use surface parcellation)rrrrz--slabel %s %s %sz&subject hemi label : use surface labelz--sum %sr z%Segmentation stats summary table file)rrpositionrz--pv %szCompensate for partial voluming)rrrz--i %sz3Use the segmentation to report stats on this volumez --frame %dz)Report stats on nth frame of input volume)rrz--mul %fzmultiply input by valz--snrz-save mean/std as extra column in output tableZsqrsqrtz--%sz/Compute either the sqr or the sqrt of the inputcolor_table_filedefault_color_tablegca_color_tablez --ctab %sz"color table file with seg id names)rrrrz--ctab-defaultz+use $FREESURFER_HOME/FreeSurferColorLUT.txt)rrrz --ctab-gca %szget color table from GCA (CMA)z --id %s...z!Manually specify segmentation idsz--excludeid %dzExclude seg id from reportz--excl-ctxgmwmz&exclude cortical gray and white matterz --surf-wm-volzCompute wm volume from surfz--surf-ctx-volzCompute cortex volume from surfz --nonemptyz"Only report nonempty segmentationsz--emptyz1Report on segmentations listed in the color tablez --mask %szMask volume (same size as segz--maskthresh %fz'binarize mask with this threshold <0.5>rnrorpz --masksign %sz)Sign for mask threshold: pos, neg, or abs)rz--maskframe %drtz1Mask with this (0 based) frame of the mask volume)rIrz --maskinvertzInvert binarized mask volumez--maskerode %dzErode mask by some amountzbrain-vol-from-segZ brainmaskzHCompute brain volume either with ``brainmask`` or ``brain-vol-from-seg``z--brainmask %szYLoad brain mask and compute the volume of the brain as the non-zero voxels in this volume)rrrz--etivz$Compute ICV from talairach transformetivzold-etivz --%s-onlyz4Compute etiv and exit. Use ``etiv`` or ``old-etiv``z --avgwf %sz2Save average waveform into file (bool or filename)z --avgwfvol %sz(Save as binary volume (bool or filename)z --sfavg %szSave mean across space and timez--vox %sz:Replace seg with all 0s except at C R S (three int inputs)z --supratentzUndocumented input flagz --subcortgrayz)Compute volume of subcortical gray matterz --totalgrayz#Compute volume of total gray matterz--eulerzHWrite out number of defect holes in orig.nofix based on the euler numberz--in %s --in-intensity-name %sz Undocumented input norm.mgz fileZMRz--in-intensity-units %s in_intensityzIntensity units)rrIrN)rrr)rrr)7r$r%r&Z _xor_inputsrrrr.r(r*rr summary_fileZpartial_volume_filerrr0framer/multiplyr1Zcalc_snrZ calc_powerZ _ctab_inputsrrrr,Z segment_idZ exclude_idZexclude_ctx_gm_wmZwm_vol_from_surfZcortex_vol_from_surfZnon_empty_onlyemptyrtrZ mask_signZ mask_frameZ mask_invertZ mask_erodeZ brain_volbrainmask_filerZ etiv_onlyravgwf_txt_file avgwf_file sf_avg_fileZvoxZ supratentZ subcort_gmZ total_grayZeulerrZintensity_unitsr2r2r2r3rs                 rc@s6eZdZedddZeddZeddZeddZdS) SegStatsOutputSpecTz%Segmentation summary statistics table)rrz7Text file with functional statistics averaged over segs)rz4Volume with functional statistics averaged over segsz>> import nipype.interfaces.freesurfer as fs >>> ss = fs.SegStats() >>> ss.inputs.annot = ('PWS04', 'lh', 'aparc') >>> ss.inputs.in_file = 'functional.nii' >>> ss.inputs.subjects_dir = '.' >>> ss.inputs.avgwf_txt_file = 'avgwf.txt' >>> ss.inputs.summary_file = 'summary.stats' >>> ss.cmdline 'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --i functional.nii --sum ./summary.stats' Z mri_segstatscCs |jj}t|jjr.tjj|jj|d<ntjjtj d|d<t dddd}t|jj rrtjj |jj \}}t|jj rdj|jj }t|jjrdj|jj}x`t|jD]P\}}t|j|}t|rt|trt||tj dd ||<qtjj|||<qW|S) Nrz summary.statsz _avgwf.txtz _avgwf.nii.gzz sfavg.txt)rrr_F)rrr)r6r7r r8rr9r:rr;r<dictrrrrlistitemsgetattrrrr)r=r>ZsufficesrsrcrArr[r2r2r3r@s,       zSegStats._list_outputscs|d kr,t|ts,tjj|s,tjjd|}|d krZt|trL|j|}n|}|j|S|dkrtjj|j j j dd}|j||fSt t |j|||S) Nrrrrrrz.mgzr)rr)rrr)rrr9r:isabsr;r@rrRr8rreplacerTrrY)r=rArZr[rZintensity_name)rWr2r3rYs    zSegStats._format_argcCs|dkr|j|SdS)Nr)r@)r=rAr2r2r3rB s zSegStats._gen_filename) r$r%r&rCrDrrErr6r@rYrBr\r2r2)rWr3rs rc@seZdZejddddddZeddddZeddd Zeddd dZ eddd dZ eddd dZ eddd dZ eddddZ eddddZeddddZeddd ZejddZdS)SegStatsReconAllInputSpecrKTz --subject %szSubject id being processed)rLrrrzInput file mri/ribbon.mgz)rrrzInput segmentation volume)rrzInput transform filezInput lh.orig.nofixzInput rh.orig.nofixz-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.pialzMandatory implicit input in 5.3zkIf running as a node, set this to True otherwise, this will copy the implicit inputs to the node directory.)rN)r$r%r&rrMrKrribbon presurf_seg transform lh_orig_nofix rh_orig_nofixlh_whiterh_whitelh_pialrh_pialasegr1rNr2r2r2r3rs4    rcs4eZdZdZeZeZfddZfddZ Z S)SegStatsReconAlla This class inherits SegStats and modifies it for use in a recon-all workflow. This implementation mandates implicit inputs that SegStats. To ensure backwards compatability of SegStats, this class was created. Examples -------- >>> from nipype.interfaces.freesurfer import SegStatsReconAll >>> segstatsreconall = SegStatsReconAll() >>> segstatsreconall.inputs.annot = ('PWS04', 'lh', 'aparc') >>> segstatsreconall.inputs.avgwf_txt_file = 'avgwf.txt' >>> segstatsreconall.inputs.summary_file = 'summary.stats' >>> segstatsreconall.inputs.subject_id = '10335' >>> segstatsreconall.inputs.ribbon = 'wm.mgz' >>> segstatsreconall.inputs.transform = 'trans.mat' >>> segstatsreconall.inputs.presurf_seg = 'wm.mgz' >>> segstatsreconall.inputs.lh_orig_nofix = 'lh.pial' >>> segstatsreconall.inputs.rh_orig_nofix = 'lh.pial' >>> segstatsreconall.inputs.lh_pial = 'lh.pial' >>> segstatsreconall.inputs.rh_pial = 'lh.pial' >>> segstatsreconall.inputs.lh_white = 'lh.pial' >>> segstatsreconall.inputs.rh_white = 'lh.pial' >>> segstatsreconall.inputs.empty = True >>> segstatsreconall.inputs.brain_vol = 'brain-vol-from-seg' >>> segstatsreconall.inputs.exclude_ctx_gm_wm = True >>> segstatsreconall.inputs.supratent = True >>> segstatsreconall.inputs.subcort_gm = True >>> segstatsreconall.inputs.etiv = True >>> segstatsreconall.inputs.wm_vol_from_surf = True >>> segstatsreconall.inputs.cortex_vol_from_surf = True >>> segstatsreconall.inputs.total_gray = True >>> segstatsreconall.inputs.euler = True >>> segstatsreconall.inputs.exclude_id = 0 >>> segstatsreconall.cmdline 'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --brain-vol-from-seg --surf-ctx-vol --empty --etiv --euler --excl-ctxgmwm --excludeid 0 --subcortgray --subject 10335 --supratent --totalgray --surf-wm-vol --sum ./summary.stats' cs.|dkr|jtjj|Stt|j|||S)Nr)rr9r:rRrTrrY)r=rArZr[)rWr2r3rYcszSegStatsReconAll._format_argc s|jjrtj|j_d|kr*|jj|d<t||jjddt||jjddt||jjddt||jj ddt||jj ddt||jj ddt||jj d d t||jj d d t||jjd d t||jjtjjd d dt||jjd t||jjd tt|jf|S)NrPrQz lh.orig.nofixz rh.orig.nofixzlh.whitezrh.whitezlh.pialzrh.pialZmriz ribbon.mgzzaseg.presurf.mgzzaseg.mgzZ transformsz talairach.xfm)r8rNr9r<rPrrrrrrrrrrrr:r;rrrTrrU)r=r8)rWr2r3rUhs*    zSegStatsReconAll.run) r$r%r&rCrrErr6rYrUr\r2r2)rWr3r9s % rc @sXeZdZeeddddDddd d Zedd dEdFddddZedddGddddZej ddHdddZ edddddZ edddIddZ edddJd dZ ej d!dKd"d#Zej d$d%d&Zejd'd(d)d*d&Zejd+d,d&Zejejd-d.ejejejd/dLd0d1Zejd2d3d&Zejd4d5d6d7d&Zejd8d9d&Zed:dd;d<Zed=d>d&Zed?d@d&Zej dAdBd&ZdCS)MLabel2VolInputSpecT)rz --label %s...rk annot_fileseg_file aparc_asegFzlist of label files)rrr^rrz --annot %srKr+zsurface annotation file)rrrrIrr^rz--seg %szsegmentation file)rrrrr^rz --aparc+asegz'use aparc+aseg.mgz in subjectdir as seg)rrrrz --temp %szoutput template volume)rrrrz--reg %sreg_file reg_headeridentityz+tkregister style matrix VolXYZ = R*LabelXYZ)rrrrz--regheader %szlabel template volumez --identityzset R=I)rrrz --invertmtxzInvert the registration matrix)rrgg?z--fillthresh %gzthresh : between 0 and 1z--labvoxvol %fz%volume of each label point (def 1mm3)rnfracz--proj %s %f %f %fzproject along surface normal)rrIrz --subject %sz subject idrrz --hemi %szhemisphere to use lh or rhz --surf %szuse surface instead of whitez--o %sz output volume)rrrz --hits %sz)file with each frame is nhits for a labelz--label-stat %sz&map the label stats field into the volz--native-vox2rasz5use native vox2ras xform instead of tkregister-styleN)rkrrr)rkrrr)rKr+)rkrrr)rkrrr)rrr)rrr)rrr)rKr+)r$r%r&r rrkrrrr1rZ template_filerrrZ invert_mtxrsZ fill_threshr/Zlabel_voxel_volumer.r*projr(rKr+surfacevol_label_fileZlabel_hit_fileZmap_label_statZnative_vox2rasr2r2r2r3rs      rc@seZdZedddZdS)Label2VolOutputSpecTz output volume)rrN)r$r%r&rrr2r2r2r3rsrc@s,eZdZdZdZeZeZddZ ddZ dS) Label2VolauMake a binary volume from a Freesurfer label Examples -------- >>> binvol = Label2Vol(label_file='cortex.label', template_file='structural.nii', reg_file='register.dat', fill_thresh=0.5, vol_label_file='foo_out.nii') >>> binvol.cmdline 'mri_label2vol --fillthresh 0.5 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii' Z mri_label2volcCs|jj}|jj}t|sxJd D]B}tt|j|r"t|j|}t|trT|d}tj j |\}}q"Wt|jj rxd}t |dtj dd}||d <|S) Nrkrrrzaparc+aseg.mgzz _vol.nii.gzF)rrrr)rkrr)r6r7r8rr rrrr9r:rrrr<)r=r>r?keyr:rrr2r2r3r@s     zLabel2Vol._list_outputscCs|dkr|j|SdS)Nr)r@)r=rAr2r2r3rBs zLabel2Vol._gen_filenameN) r$r%r&rCrDrrErr6r@rBr2r2r2r3rs  rc @seZdZejejdddddddZedddd Zed d dd d Z eddddZ eddddZ ejdddZ ej dddZej dddZeeddddd dd dZdS)!MS_LDAInputSpecz-lda %sTr z pair of class labels to optimize)rrZminlenmaxlenseprz -weight %sz.filename for the LDA weights (input or output))rrrFz -synth %sz*filename for the synthesized output volume)rrrrz -label %szfilename of the label volume)rrrz-mask %sz!filename of the brain mask volumez -shift %dz1shift all values equal to the given value to zero)rrz-conformzBConform the input volumes (brain mask typically already conformed)z-Wz7Use the weights from a previously generated weight file)rz%szlist of input FLASH imagesr )rrr^rrNr)r$r%r&rr,r0Z lda_labelsrrcvol_synth_filerkrtshiftr1Zconform use_weightsr Zimagesr2r2r2r3rsF    rc@s$eZdZedddZedddZdS)MS_LDAOutputSpecTr)rrN)r$r%r&rrcrr2r2r2r3r1s rcsDeZdZdZdZeZeZddZ ddZ fddZ d d Z Z S) MS_LDAaPerform LDA reduction on the intensity space of an arbitrary # of FLASH images Examples -------- >>> grey_label = 2 >>> white_label = 3 >>> zero_value = 1 >>> optimalWeights = MS_LDA(lda_labels=[grey_label, white_label], label_file='label.mgz', weight_file='weights.txt', shift=zero_value, vol_synth_file='synth_out.mgz', conform=True, use_weights=True, images=['FLASH1.mgz', 'FLASH2.mgz', 'FLASH3.mgz']) >>> optimalWeights.cmdline 'mri_ms_LDA -conform -label label.mgz -lda 2 3 -shift 1 -W -synth synth_out.mgz -weight weights.txt FLASH1.mgz FLASH2.mgz FLASH3.mgz' Z mri_ms_LDAcCst|jj}t|jjr.tjj|jj|d<ntjj|jj|d<t|jj  s\|jj dkrptjj|jj |d<|S)NrFrc) _outputsr7r r8Z output_synthr9r:rrrrc)r=r>r2r2r3r@Ls  zMS_LDA._list_outputscCs&tjjtjj|jjs"tjddS)Nz;MS_LDA: use_weights must accompany an existing weights file)r9r:rrr8rcrZ TraitError)r=r2r2r3_verify_weights_file_existsVsz"MS_LDA._verify_weights_file_existscs6|dkr"|jjdkr|jndStt|j|||S)NrTr)r8rrrTrrY)r=rArZr[)rWr2r3rY\s   zMS_LDA._format_argcCsdS)Nr2)r=rAr2r2r3rBeszMS_LDA._gen_filename)r$r%r&rCrDrrErr6r@rrYrBr\r2r2)rWr3r6s  rc@seZdZejddddddZejddddd d Zeddd d Z eddd d Z eddd d Z eddd d Z edddddZ ejddddZeddgdddddZejddddddZejd$d!Zd"S)%Label2LabelInputSpecrrz --hemi %sTzInput hemisphere)rrrrKz--trgsubject %szTarget subject)rLrrrz&Implicit input .sphere.reg)rrrz!Implicit input .whitez --srclabel %sz Source label)rrrrz--srcsubject %szSource subject namez --trglabel %s source_labelz %s_convertedFz Target label)rZ name_sourceZ name_templateZ hash_filesZkeep_extensionrrvolumez--regmethod %szRegistration method)rLrrz'If running as a node, set this to True.z+This will copy the input files to the node z directory.)rNzRIf running as a node, set this to True.This will copy the input files to the node z\If running as a node, set this to True.This will copy the input files to the node directory.)r$r%r&rr* hemisphererMrKr sphere_regrlsource_sphere_reg source_whitersource_subjectr'Zregistration_methodr1rNr2r2r2r3risD    rc@seZdZedddZdS)Label2LabelOutputSpecTz Output label)rrN)r$r%r&rr'r2r2r2r3rsrcs4eZdZdZdZeZeZddZ fddZ Z S) Label2LabelaY Converts a label in one subject's space to a label in another subject's space using either talairach or spherical as an intermediate registration space. If a source mask is used, then the input label must have been created from a surface (ie, the vertex numbers are valid). The format can be anything supported by mri_convert or curv or paint. Vertices in the source label that do not meet threshold in the mask will be removed from the label. Examples -------- >>> from nipype.interfaces.freesurfer import Label2Label >>> l2l = Label2Label() >>> l2l.inputs.hemisphere = 'lh' >>> l2l.inputs.subject_id = '10335' >>> l2l.inputs.sphere_reg = 'lh.pial' >>> l2l.inputs.white = 'lh.pial' >>> l2l.inputs.source_subject = 'fsaverage' >>> l2l.inputs.source_label = 'lh-pial.stl' >>> l2l.inputs.source_white = 'lh.pial' >>> l2l.inputs.source_sphere_reg = 'lh.pial' >>> l2l.cmdline 'mri_label2label --hemi lh --trglabel lh-pial_converted.stl --regmethod surface --srclabel lh-pial.stl --srcsubject fsaverage --trgsubject 10335' Zmri_label2labelcCs2|jj}tjj|jj|jjd|jj|d<|S)Nlabelr') rr7r9r:r;r8rPrKr')r=r>r2r2r3r@s zLabel2Label._list_outputsc s|jjrtj|j_d|kr(|jj|d<|jj}t||jjddj|t||jj ddj|t||jj ddj||jj dt||jj ddj||jj dtj j|jj|jjd}tj j|stj|tt|jf|S)NrPrQz{0}.sphere.regz {0}.white)rKr)r8rNr9r<rPrrrformatrlrrrr:r;rKisdirmakedirsrTrrU)r=r8r+ label_dir)rWr2r3rUs2      zLabel2Label.run) r$r%r&rCrDrrErr6r@rUr\r2r2)rWr3rs  rc@seZdZejddddddZejddddd d Zejd dd dZ ejd dddZ e ddddZ ej dddZej dddZe ddddZej ddZdS)Label2AnnotInputSpecrrz --hemi %sTzInput hemisphere)rrrrKz--s %szSubject name/ID)rLrrrz --l %s...zList of input label filesz--a %sz Name of the annotation to createzimplicit {hemisphere}.orig)rrrz--maxstatwinnerz$Keep label with highest 'stat' value)rrz --noverbosez+Turn off overlap and stat override messagesz --ctab %szEFile that defines the structure names, their indices, and their color)rrrz3copy implicit inputs and create a temp subjects_dir)rN)r$r%r&rr*rrMrKr,Z in_labels out_annotrorigr1Zkeep_maxZ verbose_offZ color_tablerNr2r2r2r3r s.    r c@seZdZedddZdS)Label2AnnotOutputSpecTzOutput annotation file)rrN)r$r%r&rr'r2r2r2r3rsrcs4eZdZdZdZeZeZfddZ ddZ Z S) Label2Annota Converts a set of surface labels to an annotation file Examples -------- >>> from nipype.interfaces.freesurfer import Label2Annot >>> l2a = Label2Annot() >>> l2a.inputs.hemisphere = 'lh' >>> l2a.inputs.subject_id = '10335' >>> l2a.inputs.in_labels = ['lh.aparc.label'] >>> l2a.inputs.orig = 'lh.pial' >>> l2a.inputs.out_annot = 'test' >>> l2a.cmdline 'mris_label2annot --hemi lh --l lh.aparc.label --a test --s 10335' Zmris_label2annotc s|jjrFtj|j_d|kr(|jj|d<t||jjddj|jjdtj j |jj|jj d}tj j |sttj |tt|jf|S)NrPrQz{0}.orig)rVrRr)r8rNr9r<rPrrr rr:r;rKr r rTrrU)r=r8r )rWr2r3rU)s    zLabel2Annot.runcCsR|jj}tjjt|jjt|jjdt|jj dt|jj d|d<|S)Nrrz.annotr') rr7r9r:r;strr8rPrKrr)r=r>r2r2r3r@<s   &zLabel2Annot._list_outputs) r$r%r&rCrDr rErr6rUr@r\r2r2)rWr3rs  rc @seZdZedddd&ddZedddd'dd Zedddd(d d Zej d dddd)ddZ ej ddd*ddZ ej dddddddd+dd Z ej ddddZejddd Zed!dd"d#Zejd$dd Zd%S),SphericalAverageInputSpecz%sTFr zOutput filename)rrrrrrzAverage subject)rrrrrrzInput surface file)rrrrrrrzInput hemisphere)rrrrzFilename from the average subject directory. Example: to use rh.entorhinal.label as the input label filename, set fname to 'rh.entorhinal' and which to 'label'. The program will then search for ``/label/rh.entorhinal.label``ZcoordsrvalsZcurvareazNo documentationz-o %szOutput subject id)rrrz -erode %dZ Undocumented)rrz-orig %szOriginal surface filename)rrrz-t %.1fNri)r$r%r&rr'r in_averagein_surfrr*rrMrwhichrKr0rin_origr/ thresholdr2r2r2r3rGs6rc@seZdZedddZdS)SphericalAverageOutputSpecFz Output label)rrN)r$r%r&rr'r2r2r2r3r"psr"cs<eZdZdZdZeZeZfddZ ddZ ddZ Z S) SphericalAveragea This program will add a template into an average surface. Examples -------- >>> from nipype.interfaces.freesurfer import SphericalAverage >>> sphericalavg = SphericalAverage() >>> sphericalavg.inputs.out_file = 'test.out' >>> sphericalavg.inputs.in_average = '.' >>> sphericalavg.inputs.in_surf = 'lh.pial' >>> sphericalavg.inputs.hemisphere = 'lh' >>> sphericalavg.inputs.fname = 'lh.entorhinal' >>> sphericalavg.inputs.which = 'label' >>> sphericalavg.inputs.subject_id = '10335' >>> sphericalavg.inputs.erode = 2 >>> sphericalavg.inputs.threshold = 5 >>> sphericalavg.cmdline 'mris_spherical_average -erode 2 -o 10335 -t 5.0 label lh.entorhinal lh pial . test.out' Zmris_spherical_averagecsT|dks|dkr@tjj|}xdD]}|j|d}q"W|j|Stt|j|||S)Nr rlh.rh.r)r$r%)r9r:rRrrrTr#rY)r=rArZr[rQitem)rWr2r3rYs    zSphericalAverage._format_argcCsj|dkrNt|jjd}tjj|jj|}tjj|sJtjjtj j d}|S|dkrb|j |SdSdS)Nrz .EC_averageZFREESURFER_HOMEr') rr8rr9r:r;rPr renvironr7r@)r=rAZ avg_subjectZ avg_directoryZfs_homer2r2r3rBs  zSphericalAverage._gen_filenamecCs|jj}t|jjr.tjj|jj|d<nhtjj|jj |jj d}t|jj rttjj |jj }|j ddd}nt|jjd}tjj|||d<|S)Nr'rrZ_exvivo_z.labelz.EC_exvivo_average.label)rr7r r8r'r9r:rr;rPrKrrRrrr)r=r>Zout_dirrRr2r2r3r@s   zSphericalAverage._list_outputs) r$r%r&rCrDrrEr"r6rYrBr@r\r2r2)rWr3r#ts  r#)5rCr9Zutils.filemaniprrbaserrrr r r r rrutilsrZ __docformat__rr4r5rFrOr]r}rrrrrrrrrrrrrrrrrrrrrrr rrrr"r#r2r2r2r3sV$  S%!@6RE>H$. I'HV'/32M$3)