U f{jT @s<ddlmZddlmZddlZddlZddlmZddl m Z ddl Z ddl m Z ddlZddlmZmZddlmZmZmZdd lmZmZmZmZmZmZmZdd lm Z dd l!m"Z"dd l#m$Z$dd l%m&Z&m'Z'm(Z(m)Z)m*Z*m+Z+m,Z,m-Z-m.Z.m/Z/ddl0m1Z1m2Z2m3Z3ddl4m5Z5m6Z6m7Z7m8Z8m9Z9m:Z:m;Z;mZ>m?Z?m@Z@mAZAmBZBmCZCmDZDmEZEGdddeFZGddZHddZIddZJddZKddZLddZMddZNdd#d$ZOd%d&ZPe5dd'd(ZQd)d*ZRd+d,ZSd-d.ZTdd/d0ZUd1d2ZVdd3d4ZWd5d6ZXd7d8ZYdd:d;ZZe5dd>d?Z[d@dAZ\dBdCZ]dDdEZ^dFdGZ_dHdIZ`e5ddNdOZae5ddRdSZbe5ddTdUZce5ddVdWZdddXdYZedd[d\Zfe5dd_d`ZgdadbZhe5ddcddZidedfZjdgdhZkddidjZle5ddkdlZmdmdnZndodpZoedqejpfdrejqfdsejrfdZejsfgZtejpejrejsdtZuejpduejrdvejsdwejvdxiZwejpdqejqdyejrdvejsdwejvdxiZxdzd{Zye5dd|d}Zze5ddd~ddZ{ddZ|e5dddZ}ddZ~ddZddZe5dddZe5ddd9ddddZddZdddZdddZddZeFdddZe5dddddddZe5dddZdS)) OrderedDict)partialN)Pathdeepcopy)FIFFFWD)_dig_kind_dict _dig_kind_rev_dig_kind_ints)start_and_end_file start_block write_float write_intwrite_float_matrixwrite_int_matrix end_block)find_tag) dir_tree_find) fiff_open) read_surface write_surfacecomplete_surface_info_compute_nearest_get_ico_surfaceread_tri_fast_cross_nd_sum _get_solids_complete_sphere_surfdecimate_surface) _ensure_trans apply_trans Transform)verboseloggerrun_subprocessget_subjects_dirwarn_pl_validate_type_TempDir_check_freesurfer_home _check_fname has_nibabel _check_option path_like _on_missing_import_h5io_funcs _ensure_int _path_likec@s,eZdZdZddZddZeddZdS) ConductorModelzBEM or sphere model.cCs|drbddd|dD}|j}|dkr8d|}q~dt|dd t|d||d f}nd t|d t|d f}d |S)N is_sphere, css|]}d|dVqdS)%0.1f@@N.0xr:r:F/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/bem.py 9sz*ConductorModel.__repr__..r0zSphere (no layers): r0=[%s] mmz&Sphere (%s layer%s): r0=[%s] R=%1.f mmlayersrr9zBEM (%s layer%s)surfsz)joinradiuslenr))selfcenterradextrar:r:r>__repr__7s   zConductorModel.__repr__cCst|S)z'Return copy of ConductorModel instance.rrFr:r:r>copyFszConductorModel.copycCs4|dstdt|ddkr$dS|dddS)z%Sphere radius if an EEG sphere model.r6zradius undefined for BEMrArNrH) RuntimeErrorrErKr:r:r>rDJszConductorModel.radiusN)__name__ __module__ __qualname____doc__rJrLpropertyrDr:r:r:r>r54s r5c CsZ|d|d}tj|}||}|t||}|t||}t|||}|S)z _calc_betaRs r\cCsntt|df}|tjdddf|}|tjdddf|}|tjdddf|}t|||}tjj|dd} tjj|dd} tjj|dd} | | | } | td||| 7} | td||| 7} | td||| 7} t|| } t | tj dk}d | |<d | |<d | |<t || || ddtjft || || ddtjft || || ddtjfg}|d|d|}||d|d|7}||d|d|7}d |}d ||}|||g}dddddg}t dD]}|||d|||d}t|||d|||d|}| ||d | |||j d d|dd|f<qd ||<|S) z9Compute the linear potential matrix element computations.rNrZaxisz ij,ij,i->ig.A?@rM)rTzerosrEnewaxisrrUrVZeinsumZarctan2abspir\rangesum)frostri_rrtri_nntri_areaomegaZv1Zv2Zv3Ztriplesl1l2l3sssolidsZbad_maskbetaZ vec_omegaZarea2Zn2ZyysidxkdiffZzdotsr:r:r>_lin_pot_coeff]sH       $rwcCsdtj}|d}||jdd}t|D]\}}t|d|}|dksRt|d|||f<|d|}t||kd}|d} tdd gd dgd d gg} || | df} || | df} t | | D]8\} }|||| f|7<||||f|7<qq.d S) z#Improve auto-element approximation.ratrisrr_ neighbor_trirg@r]r^rMN) rTrfravelrh enumeraterEAssertionErrorwherearrayzip)surfZmatpi2Z tris_flatmissesjZmissZn_membmembersZmodsoffsetsZtri_1Ztri_2t1t2r:r:r>_correct_auto_elementss"    rc Csdd|D}t|}t||f}ttdg|f}t|D]J\}}t||}t|D](\}} tdt |d||t | d||f| d| d} | d} | d } |||||d ||||d f} t | d D]}| d|}||kr2||dk||d kB||d kB}nt }t |d| || || |d }d||<| dd|f|8<q||krbt || qbqB|S)z;Calculate the coefficients for linear collocation approach.cSsg|] }|dqSrTr:r<rr:r:r> sz*_fwd_bem_lin_pot_coeff..rz %s (%d) -> %s (%d) ...idrrrxrkrlrntrir^)rirjrkrlrbN)rhrTrccumsum concatenater|aranger%info_bem_surf_namerglistrwr)rBnpsZnp_totcoeffrsi_1Zsurf1Zrr_ordsi_2Zsurf2rjrkrlZsubmatrutriZskip_idxcoeffsr:r:r>_fwd_bem_lin_pot_coeffsL       rc Csddtj}t|}|j||fks*tt|}d|}ttdg|f}t|D]v}t|D]h} |dkrt|n|||| f} t ||||d} t || || d} ||| | f| || | f<qdqX|t |7}tj |S)zDo multi surface solution. * Invert I - solids/(2*M_PI) * Take deflation into account * The matrix is destroyed after inversion * This is the general multilayer case r`r^rNr) rTrfrhshaper}rErrrgsliceeyerUinv) rrgammarrZn_totZnsurfZdeflrrrmultZslice_jZslice_kr:r:r>_fwd_bem_multi_solutions    rcCst|d|dS)zMake a homogeneous solution.N)rr)r)rrrr:r:r>_fwd_bem_homog_solutionsrc Cs|d}d||}tdttdg|f}tt|D]F}|||||dt|dddf}|dt||8}q@|| d| df||7<td||9}dS) z1Modify the solution according to the IP approach.rMr`z Combining...rrNr^z Scaling...) r%rrTrrrgrErhrW) solution ip_solutionip_multn_triZn_lastrrsisubr:r:r>_fwd_bem_ip_modify_solutions  .$ rFraisecCst||dd}tdd|dDd}t|dkrt|}t|dkr\|dddgn|}d d d |D}d t|d t|t|d||}t||dd|S)NF)rLr$cSsg|]}t|dkqSr])rE)r<tr:r:r>rsz+_check_complete_surface..ryrP...r7css|]}t|VqdSN)str)r<fr:r:r>r? sz*_check_complete_surface..zoSurface {} has topological defects: {:.0f} / {:.0f} vertices have fewer than three neighboring triangles [{}]{}rr on_defects)Z on_missingmsgname) rrTr~rErrCformatrr1)rrL incompleterIZfewerrr:r:r>_check_complete_surfaces "  rcCs$|dD] }t|qtdtdt|d}t||d<tddd|dD}t||d||d <t|dd kr |d d |d d }|tjkr tdtdt|ddg}tdt||dddg}tdt |d |||tj |d<tddS)z2Compute the linear collocation potential solution.rBz,Computing the linear collocation solution...z Matrix coefficients...nsolz' Inverting the coefficient matrix...cSsg|] }|dqSrr:rr:r:r>r sz8_fwd_bem_linear_collocation_solution..rrr]sigmarr^zIP approach required...z" Matrix coefficients (homog)...rMz/ Inverting the coefficient matrix (homog)...rTz> Modify the original solution to incorporate IP approach... bem_methodzSolution ready.N) rr%rrrErr ZBEM_IP_APPROACH_LIMITrrBEM_LINEAR_COLL)bemrrrrrr:r:r>$_fwd_bem_linear_collocation_solutions2              rcCs|tdt|}t|t|ddkr6tdn$t|ddkrRtdntdt|dt|td|S) aCreate a BEM solution using the linear collocation approach. Parameters ---------- surfs : list of dict The BEM surfaces to use (from :func:`mne.make_bem_model`). %(verbose)s Returns ------- bem : instance of ConductorModel The BEM solution. See Also -------- make_bem_model read_bem_surfaces write_bem_surfaces read_bem_solution write_bem_solution Notes ----- .. versionadded:: 0.10.0 z*Approximation method : Linear collocation rBr]"Three-layer model surfaces loaded.r!Homogeneous model surface loaded.z-Only 1- or 3-layer BEM computations supportedz#BEM geometry computations complete.)r%r_ensure_bem_surfaces_add_gamma_multipliersrErN_check_bem_sizer)rBr$rr:r:r>make_bem_solution3s     rc Cst|d}d||f}|ddkr,t||d}ttt|td}|d|krdt|~||kr~td||ft|}t|dd}|d =|d =|d =|d =t|d|dstd t d||t|dt|df|dt |||d<|S)zADownsample the surface if isomorphic to a subdivided icosahedron.rxzCannot decimate to requested ico grade %d. The provided BEM surface has %d triangles, which cannot be isomorphic with a subdivided icosahedron. Consider manually decimating the surface to a suitable density and then use ico=None in make_bem_model.rz@For this surface, decimation grade should be %d or less, not %s.T) patch_statsZtri_centrkryrlzKThe source surface has a matching number of triangles but ordering is wrongzGGoing from %dth to %dth subdivision of an icosahedron (n_tri: %d -> %d)r) rErNintroundrTrXrZ array_equalr%r _get_ico_map)rZ dest_graderZbad_msgfoundsourcedestr:r:r>_ico_downsample`s<     rcCs>t|d|ddd\}}|dk}|dkr:td||S)z#Get a mapping between ico surfaces.rTZ return_distsg{Gzt?rz.No matching vertex for %d destination vertices)rrhrN)frotoZnearestdistsZn_badsr:r:r>rs rcsxtdkrStjtjtjg}tddDtt|krPtdfdd|D}fdd|DS)zReorder the surfaces.r]cSsg|] }|dqSrr:rr:r:r>rsz#_order_surfaces..zbad surface ids: %scs"g|]}t|kddqS)r)rTr~)r<id_)idsr:r>rscsg|] }|qSr:r:)r<rtrBr:r>rs) rErFIFFV_BEM_SURF_ID_HEADFIFFV_BEM_SURF_ID_SKULLFIFFV_BEM_SURF_ID_BRAINrTrsetrN)rBZ surf_orderorderr:)rrBr>_order_surfacess  rc Cs|djdd}tdt|dd|dd|dd|dft|d|d |tjd d fd}|dtj}t|d d krd t|dd|d}t ||dt dd S)z2Check the sum of solid angles as seen from inside.rrr_z%s CM is %6.2f %6.2f %6.2f mmrrr^rxNr`h㈵>Surface z. is not complete (sum of solid angles yielded z, should be 1.)r)rZ error_klass) meanr%rrrrTrdrfrer1rN)rrcm tot_angleproprr:r:r>_assert_complete_surfaces$  (rcCst|d}t|d}td|d|dt|d|d|d}t|dtjdd kr~td |d |d S) z,Check one set of points is inside a surface.rzChecking that surface z is inside surface z ...rrxr^r`rrz" is not completely inside surface N) rr%rrrTrerfanyrN)rrZfro_nameZto_namerr:r:r>_assert_insides   rcCsH|D]}t||dqt|dd|ddD]\}}t||q0dS)z:Check that the surfaces are complete and non-intersecting.rNrMr)rrr)rBrrsurf_1surf_2r:r:r>_check_surfacess"rcCsX|djdd|djdd}|dkrTtdt|ddd|d d d S) z0Check that the coordinate limits are reasonable.rrr_g?zDimensions of the surface rz seem too small (rz9.5fz4). Maybe the unit of measure is meters instead of mmN)maxminrrNr)rsizesr:r:r>_check_surface_sizes   "rc Cst|dd|ddD]~\}}t|d|dddd}|}t|d}t|d}td|d |d td |d |d d |ddqdS)zCompute how close we are.NrMrrTrrzChecking distance between z and z surfaces...zMinimum distance between the z surfaces is approximately rz6.1fz mm)rrrrr%r)rBrrZmin_distrrr:r:r>_check_thicknessess"  rTc Cs^t|dks.t|t|kr,t|ks6ntdt|D]*\}}t|tr>t|ddd||<}q>|dk rt|D]\}}t||||<qzt||D]d\}} | |d<t|d||d| d t j |d <|j t|d t|d d |r|d d <qt||D]\}} | |d<q t |}t||d|D]}t|q8t|td|S)zConvert surfaces to a BEM.rr]zIsurfs, ids, and sigmas must all have the same number of elements (1 or 3)T)Z return_dictrMNr)rLrrI coord_framerrx)rTrr9rrz*Surfaces passed the basic topology checks.)rE ValueErrorr| isinstancerrrrrgetrFIFFV_COORD_MRIupdaterrrrr%r) rBrsigmasicorescalerrIrrrrr:r:r>_surfaces_to_bems8      rr333333?g~jtx?rc Cst|t}|jdks |jdkr(tdt|dd}t||}t|d}t|d}t|d}t|d } ||| g} t j t j t j g} t d t|dkr| d d} | d d} t| | ||} t| t d | S) aCreate a BEM model for a subject. .. note:: To get a single layer bem corresponding to the --homog flag in the command line tool set the ``conductivity`` parameter to a list/tuple with a single value (e.g. [0.3]). Parameters ---------- subject : str The subject. ico : int | None The surface ico downsampling to use, e.g. 5=20484, 4=5120, 3=1280. If None, no subsampling is applied. conductivity : array of int, shape (3,) or (1,) The conductivities to use for each shell. Should be a single element for a one-layer model, or three elements for a three-layer model. Defaults to ``[0.3, 0.006, 0.3]``. The MNE-C default for a single-layer model would be ``[0.3]``. %(subjects_dir)s %(verbose)s Returns ------- surfaces : list of dict The BEM surfaces. Use `make_bem_solution` to turn these into a `~mne.bem.ConductorModel` suitable for forward calculation. See Also -------- make_bem_solution make_sphere_model read_bem_surfaces write_bem_surfaces Notes ----- .. versionadded:: 0.10.0 rrz7conductivity must be 1D array-like with 1 or 3 elementsTZ raise_errorrzinner_skull.surfzouter_skull.surfzouter_skin.surfzCreating the BEM geometry...Nz Complete. )rTrfloatndimrYrr'oprCrrrrr%rrErr) subjectrZ conductivity subjects_dirr$ subject_dirbem_dir inner_skull outer_skull outer_skinZsurfacesrr:r:r>make_bem_models,)             r c Cst|d}|dkrdSt|d}t|d}t|d}t|d}t|dD]p}|d|d|d|dd||<||d||<|d|d||<||||<||||9<q\t|d}td|D]} t|dD]}||||9<qtd} | d} t|dddD]V}t| | ||| ||||g| ||||| | ||gg| } q2| d | d|d} | | | d | | d || d<q|S) z.Get the model depended weighting factor for n.rA)rrr`rrrel_radr^rMra)rr)rr)rErTrcrgrrW) mZn_termsZnlayerc1c2crZcr_multrurnMZn1rZr:r:r>&_fwd_eeg_get_multi_sphere_model_coeffsKs8 (  &"&rc Csddlm}td|d}|d|}|ddd|ddd||dd}|dddtjf|dd|ddtjf|ddtjf}|j|d d \}}} |d d} |ddd| f|d| | d| }}} |||| fS) zGet the linear fitting data.r)rUrntermswNrMfnF)Z full_matricesnfit)ZscipyrUrTrrdZsvd) muurUZk1Zmu1nsyruusingvvZncompr:r:r>_compose_linear_fitting_datans  00 0rc Cst||\}}}}t||}|t||}||}t|d}t|||dd<|ddt|dd|d<t||t||} | |fS)z+Compute the best-fitting linear parameters.rrNrr)rrTrWrcrh) rrrrrrZvecresilambda_rvr:r:r>_compute_linear_parameters~s "r!cCsLt|dkrdSt||\}}}}|t|t||}t||S)zBEvaluate the residual sum of squares fit for one set of mu values.r`gY@)rTrerrrW)rrrrrrrr:r:r> _one_steps r"cs\ddlm}|dkstt||d}t||d|d<tdd|d Dtd d|d D}td|d}t d |dd |d |t ||d |d<d|dd<t d}t t |d}d} d d| fdd} |||| gdd| d} t| |\} } t| ddd}| || |} } | |d<| |d dd|d<||d<| S)zAFit the Berg-Scherg equivalent spherical model dipole parameters.r fmin_cobylar^)rrrrcSsg|] }|dqSrHr:r<layerr:r:r>rsz,_fwd_eeg_fit_berg_scherg..rAcSsg|] }|dqSr%r:r&r:r:r>rsrag@r`rrMr])rư>cst|Sr)rTre)r=Zmax_r:r>conssz&_fwd_eeg_fit_berg_scherg..consg?r)rhobegrhoendcatolNrrlambdar)scipy.optimizer$r}dictrrrrTrsqrtpowerrcrr"r!argsort)r rrr$rrruZmu_0Zfunr-r*rr rrr:r)r>_fwd_eeg_fit_berg_schergs6        r4rbrbg{Gz? ףp= ?g?gq= ףp?g ףp= ?r`Q?r`gMbp?r9c CsdD]0}t|}t|tr|dkrtd||fqt|t}t|t}t|t|kr~tdt|t|ft|dkr|dk rtdt|ft|tr|dkst|tr|dkr|dkrtdt |d d dd \}} t|tr| }t|tr|}t d t|t j d } t | d<|dk rt|t}t|t}t|} || }|| }t||D]4\} } t| | d}| |d<|d<| d|qz| ddd}| ddd}| dD]&}|d|<|d|<qtt|D]&}|| d|d| d|d<q t| dd}tdd|tdD]D}td|d| d||d| ddd| d|fqZtdd|f| S)uCreate a spherical model for forward solution calculation. Parameters ---------- r0 : array-like | str Head center to use (in head coordinates). If 'auto', the head center will be calculated from the digitization points in info. head_radius : float | str | None If float, compute spherical shells for EEG using the given radius. If 'auto', estimate an appropriate radius from the dig points in Info, If None, exclude shells (single layer sphere model). %(info)s Only needed if ``r0`` or ``head_radius`` are ``'auto'``. relative_radii : array-like Relative radii for the spherical shells. sigmas : array-like Sigma values for the spherical shells. %(verbose)s Returns ------- sphere : instance of ConductorModel The resulting spherical conductor model. See Also -------- make_bem_model make_bem_solution Notes ----- The default model has:: relative_radii = (0.90, 0.92, 0.97, 1.0) sigmas = (0.33, 1.0, 0.004, 0.33) These correspond to compartments (with relative radii in ``m`` and conductivities σ in ``S/m``) for the brain, CSF, skull, and scalp, respectively. .. versionadded:: 0.9.0 )r@ head_radiusautoz#%s, if str, must be "auto" not "%s"z9relative_radii length (%s) must match that of sigmas (%s)rNzEat least 2 sigmas must be supplied if head_radius is not None, got %sz#Info must not be None for auto moder )unitsr^T)r6r@rrA)rHrr rHrMr]z# Equiv. model fitting -> RV = %g %%dzmu%d = %g lambda%d = %grrr.z3Set up EEG sphere model with scalp radius %7.1f mm r)localsrrrrTrrr{rEfit_sphere_to_headshaper5rFIFFV_COORD_HEADrr3rr0appendrgr4r%r)r@r:rZrelative_radiirr$rparamZhead_radius_fitZr0_fitZsphererr sigr'RZrRrur r:r:r>make_sphere_models-                rFr;r cCsTt|tr|dkrtdt||\}}}|dkrJ|d9}|d9}|d9}|||fS)aUFit a sphere to the headshape points to determine head center. Parameters ---------- %(info_not_none)s %(dig_kinds)s units : str Can be "m" (default) or "mm". .. versionadded:: 0.12 %(verbose)s Returns ------- radius : float Sphere radius. origin_head: ndarray, shape (3,) Head center in head coordinates. origin_device: ndarray, shape (3,) Head center in device coordinates. Notes ----- This function excludes any points that are low and frontal (``z < 0 and y > 0``) to improve the fit. )r mmzunits must be a "m" or "mm"rGr9)rrr_fit_sphere_to_headshape)r dig_kindsr<r$rD origin_head origin_devicer:r:r>r@6s r@c spt|d|ddkrtdttrbdkr\z t|dWStk rPYnXt|dSfttD]B\}}t |||<|t krrtd||t tt fqrfd d |dD}t d d |dDrtd |rdd |D}t|}t|dkrlddd t D}dt|t|f}t|dkr`t|dn t|d|S)aGet digitization points suitable for sphere fitting. Parameters ---------- %(info_not_none)s %(dig_kinds)s %(exclude_frontal)s Default is True. .. versionadded:: 0.19 %(verbose)s Returns ------- dig : array, shape (n_pts, 3) The digitization points (in head coordinates) to use for fitting. Notes ----- This will exclude digitization locations that have ``z < 0 and y > 0``, i.e. points on the nose and below the nose on the face. .. versionadded:: 0.14 rdigNz?Cannot fit headshape without digitization , info["dig"] is Noner;rI)rIZeegz%dig_kinds[#%d] (%s) must be one of %scs g|]}|dkr|dqS)kindrr:r<prIr:r>rs z#get_fitting_dig..css|]}|dtjkVqdS)rN)rrArOr:r:r>r?sz"get_fitting_dig..zJDigitization points not in head coordinates, contact mne-python developerscSs(g|] }|ddkr |ddks|qS)r^gưrr(r:rOr:r:r>rs r7cSsg|]}dt|qS)z"%s")r )r<dr:r:r>rsz>Only %s head digitization points of the specified kind%s (%s,)rz, at least 4 requiredz, fitting may be inaccurate)r*rNrrget_fitting_digrrr|r rr sortedkeysrrTrrErCr)r() rrIZexclude_frontalr$ZdirShspZ kinds_strrr:rQr>rT]sF         rTc Cst||}tt|dd\}}|d}|dkr:tdd}t|dd}t||}td dd |d f|d krt d d |ftj |dd dkrt dt d |dd td ddt d |td ddt d ||||fS)z%Fit a sphere to the given head shape.F)disp dev_head_tNmegheadzFitted sphere radius:z%0.1f mmr9g)\(?zKEstimated head size (%0.1f mm) exceeded 99th percentile for adult head sizer^g{Gz?z@(X, Y) fit (%0.1f, %0.1f) more than 20 mm from head frame originzOrigin head coordinates:z%0.1f %0.1f %0.1f mmzOrigin device coordinates:)rT _fit_sphererTrr#r!r"r%rljustr(rUrVtuple) rrIr$rWrDrJrYZ head_to_devrKr:r:r>rHs2      rHc sddlm}t|tr0|dkr0tjdkr,dnd}tjddtjddd }| }tj dd}t ||gg}fd d }d d }||||||d|d} | dd| d} } | | fS)z+Fit a sphere to an arbitrary set of points.rr#r;rTFrr_racs4tjj|dddd|d}||9}|S)Nr]rr_)rTrUrVrh) center_radrSpointsr:r>cost_funs$z_fit_sphere..cost_funcSs|dS)Nr]r:)r`r:r:r> constraintsz_fit_sphere..constraintr()r+r,rXNr]) r/r$rrr%levelrTrrrZmedianr) rbrXr$ZradiiZ radius_initZ center_initZx0rcrdZx_optoriginrDr:rar>r]s    r]r[cCst|tr^|dkr td|f|dkrZt|ddddd\}}td |d f~nd }t|t}|j d kr|td |rd dd|D}d||f}|dkr|ddk rt |d|}d dd|D}|d|f7}t||S)z#Check or auto-determine the origin.r;z3origin must be a numerical array, or "auto", not %sr[Fr )r$r<Nr^z1 Automatic origin fit: head of radius %0.1f mmr9)rbrbrbrz origin must be a 3-element arrayr7cSsg|]}d|dqS)r8rr:r<or:r:r>rsz!_check_origin..z& Using origin %s mm in the %s framerZrYcss|]}d|dfVqdS)r8rNr:rgr:r:r>r?sz _check_origin..z (%s mm in the head frame)) rrrr@r%rrTrrrrCr")rfrrrXrEZ origin_strrZo_devr:r:r> _check_origins<     riT1ws.mgzc $ Csrddlm} t||\} }}t}tt| |d}| d}t||}t|d}t||}|}|dsr|d7}t |st |t |ddd d t |r|st d |n t|d g}|r|d dt|g7}| dkr|} | r|dg7}|rNt| ddd}tt|dddd}td|f|dd||dg7}n|r^|dg7}t|r|ddt|||t|| g7}n"|ddt|||t|| g7}td|d|ft t|||~t|rtrt|nt}|stddd d!d"g}|D]}t|d#||f}t|dd$\}}}||t||||dd%t|d&|}|st|rd} n&t|rt |t|||d'} q"| rtd(t|d}!ntd)|}!td*|!t||d+}"t|"rt |"t t||d,gt!j"gdgd-}#t#|"|#|r^| ||d.ddd/td0|"fdS)1aCreate BEM surfaces using the FreeSurfer watershed algorithm. Parameters ---------- subject : str Subject name. %(subjects_dir)s %(overwrite)s volume : str Defaults to T1. atlas : bool Specify the --atlas option for mri_watershed. gcaatlas : bool Specify the --brain_atlas option for mri_watershed. preflood : int Change the preflood height. show : bool Show surfaces to visually inspect all three BEM surfaces (recommended). .. versionadded:: 0.12 copy : bool If True (default), use copies instead of symlinks for surfaces (if they do not already exist). .. versionadded:: 0.18 .. versionchanged:: 1.1 Use copies instead of symlinks. T1 : bool | None If True, pass the ``-T1`` flag. By default (None), this takes the same value as ``gcaatlas``. .. versionadded:: 0.19 brainmask : str The filename for the brainmask output file relative to the ``$SUBJECTS_DIR/$SUBJECT/bem/watershed/`` directory. Can be for example ``"../../mri/brainmask.mgz"`` to overwrite the brainmask obtained via ``recon-all -autorecon1``. .. versionadded:: 0.19 %(verbose)s See Also -------- mne.viz.plot_bem Notes ----- If your BEM meshes do not look correct when viewed in :func:`mne.viz.plot_alignment` or :func:`mne.viz.plot_bem`, consider potential solutions from the :ref:`FAQ `. .. versionadded:: 0.10 rplot_bemenvcwd SUBJECTS_DIRZ watershed.mgzreadTzMRI data) overwriteZ must_existrz=%s already exists. Use the --overwrite option to recreate it.Z mri_watershedz-hz%sNz-T1FREESURFER_HOMEZaveragezRB_all_withskull_*.gcarMrzUsing GCA atlas: %sz-atlasz -brain_atlasz(/mri/transforms/talairach_with_skull.ltaz-useSRASz-surfzj Running mri_watershed for BEM segmentation with the following parameters: Results dir = %s Command = %s  zfnibabel is not available or the volumn info is invalid.Volume info not updated in the written surface.brainrrr z %s_%s_surface)Z read_metadata) volume_infortz%s.surfFjUnable to create all symbolic links to .surf files in bem folder. Use --overwrite option to recreate them.3Symbolic links to .surf files created in bem folderzY Thank you for waiting. The BEM triangulations for this subject are now available at: %s.z -head.fifZ_outer_skin_surface)rcoronalrrZ orientationZslicesshowzCreated %s Complete.)$viz.miscrm _prepare_envr+rr&rrCendswithisdirosmakedirsr-rNshutilrmtreerrUglobr%rexistsisfiler._extract_volume_infor0r(rrrremove_symlinkrrrwrite_bem_surfaces)$rrrtvolumeZatlasZgcaatlasZprefloodr}rLrjZ brainmaskr$rmromri_dirrtempdirrun_subprocess_envrZws_dirT1_dirZT1_mgzcmdfnameZnew_inforBsZ surf_ws_outrrxrxZsurf_out skip_symlinkrZ fname_headrr:r:r>make_watershed_bems:                             rcCsddl}||j}|d}t}|dkrd|}||d<||d<|ddd |d <|d |d <|d \|d<|d<|d<|d|d<|S)z$Extract volume info from a mgz file.rNversionrz%s # volume info validZvalidfilenamedimsr]rdeltaZ voxelsizeZMdcZxrasZyrasZzrasZPxyz_cZcras)nibabelloadheaderr0)ZmgzrrrZvol_infor:r:r>rs   rcCst|ddt|ddd}|dr0t||}n t||}|dk rZt|dkrZtd ||D] }|sr|d dkr^t||d q^|dk r|d S|S) aRead the BEM surfaces from a FIF file. Parameters ---------- fname : str The name of the file containing the surfaces. patch_stats : bool, optional (default False) Calculate and add cortical patch statistics to the surfaces. s_id : int | None If int, only read and return the surface with the given s_id. An error will be raised if it doesn't exist. If None, all surfaces are read and returned. %(on_defects)s .. versionadded:: 0.23 %(verbose)s Returns ------- surf: list | dict A list of dictionaries that each contain a surface. If s_id is not None, only the requested surface will be returned. See Also -------- write_bem_surfaces, write_bem_solution, make_bem_model )zint-likeNs_idrsTr.h5Nrzsurface with id %d not foundnnrr)r*r-r_read_bem_surfaces_h5_read_bem_surfaces_fifrErr)rrrrr$rthisr:r:r>read_bem_surfacess     rcslt\}}||}zdd|dDWntk rDtdYnX|d}dk rhfdd|D}|S)NcSsg|] }|dqSrr:r<rr:r:r>rsz)_read_bem_surfaces_h5..rBBEM data not foundcsg|]}|dkr|qSrr:rrr:r>rs )r2 Exceptionr)rr read_hdf5_rrr:rr>rs rc stjt|\}}}|t|tj}|dks:t|dkrBtd|d}t|tj}|dkrftdt dt|t |tj }|dk r|j dk r‡fdd|D}dd|D}nLt }|D].} t dt| } || t d qt d t|W5QRX|S) NrrzBEM surface data not foundz %d BEM surfaces foundcsg|]}t|qSr:)_read_bem_surface)r<bsurfrfidrr:r>r sz*_read_bem_surfaces_fif..cSsg|]}|dk r|qSrr:rr:r:r>rsz Reading a surface...[done]z %d BEM surfaces read)rrrr FIFFB_BEMrErFIFFB_BEM_SURFr%rrFIFF_BEM_COORD_FRAMEdatarrrB) rrrtreerrZbemsurftagrrrr:rr>rs6      rcCs.t}t||tj}|dkr(tj|d<nt|j|d<|dk rN|d|krNdSt||tj}|dkrhdnt|j|d<t||tj }|dkrt dt|j|d<t||tj }|dkrt dt|j|d<t||tj }|dkrt||tj }|dkr||d <n |j|d <n |j|d <t||tj}|dkr>t d |jtj|d <|d jd |dkrpt d t||tj}|dkrt||tj}|dkrd|d<n2|jtj|d<|djd |dkrt dt||tj}|dkrt d|jd|d<|djd |dkr*t d|S)zRead one bem surface.Nrr`rzNumber of vertices not foundrTzNumber of triangles not foundrrzVertex data not foundrrzVertex information is incorrectrz&Vertex normal information is incorrectzTriangulation not foundrrxz&Triangulation information is incorrect)r0rrFIFF_BEM_SURF_IDFIFFV_BEM_SURF_ID_UNKNOWNrrFIFF_BEM_SIGMArFIFF_BEM_SURF_NNODErFIFF_BEM_SURF_NTRIFIFF_MNE_COORD_FRAMErFIFF_BEM_SURF_NODESZastyperTZfloat64rZFIFF_MNE_SOURCE_SPACE_NORMALSFIFF_BEM_SURF_NORMALSFIFF_BEM_SURF_TRIANGLES)rrZdef_coord_framerr[rr:r:r>rsZ           rc s0t|ddd}|dr6t\}}td||}nt|}t|ddkrtdtt j t j t j gt fd d |dDstd d gd}|dD]"}||t|d kdd<q||d<nr?sz$read_bem_solution..z%Could not find necessary BEM surfacesNrrrzBEM Surfaces not foundrrBrrFr6zBEM approximation methodrrTrrr^zJExpected a two-dimensional solution matrix instead of a %d dimensional onez;Expected a %d x %d solution matrix instead of a %d x %d onerzconstant collocationZlinear_collocationzLoaded %s BEM solution from %s)r-rr2r%r_read_bem_solution_fifrErTrrrrrallrNr~rrVr}r5r/FIFFV_BEM_APPROX_LINEARZFIFFV_BEM_APPROX_CONSTrr) rr$rrrZreorderr=dimrrrMr:rr>read_bem_solution`sj              rc Cstdt|ddd}tdt|\}}}|r}t|tj}t|dkrZtd||d}t ||tj }|dkrtd||j d} t ||tj }|j } W5QRXt | | |d S) NzLoading surfaces...TF)rr$z Loading the solution matrix... rzNo BEM data in %szNo BEM solution found in %s)rrrB)r%rrrrrrrErNrFIFF_BEM_APPROXrFIFF_BEM_POT_SOLUTIONr0) rrBrrrrnodesZbem_nodermethodZsolr:r:r>rs        rcCstdd|dD|d<tjd|df}d|dd|dd |d <|dd|dd |d <t|dt|d kst|dd|dd tjddf|dd|dd ddtjf|d <dS) z#Add gamma and multipliers in-place.cSsg|] }|dqS)rr:rr:r:r>rsz*_add_gamma_multipliers..rBrrbrarNrMZ source_multZ field_multr)rTrZr_rEr}rd)rrr:r:r>rs $$rrwrr)rrr[z inner skullz outer skullz outer skin z unknown ZcsfcCs|drt}t}d}d}nt}t}d}d}t|trB|}||}n||}|drVdnd}ttdd|dD|kd }t |d krt |d |d ||d|d S) z1Find surface from already-loaded conductor model.r6z Sphere modelboundaryZBEMZ triangulationcSsg|] }|dqSrr:rr:r:r>rsz%_bem_find_surface..rBrrz does not have the rv) _sm_surf_dict _sm_surf_name_bem_surf_dictrrrrTr~rrErN)rrZ _surf_dictZ _name_dictrMrrrtr:r:r>_bem_find_surfaces$  & rc Cst|tr|g}t||dd}|drHt\}}||t|dddnLt|>}t|tjt |tj |ddt ||t |tjW5QRXd S) aWrite BEM surfaces to a fiff file. Parameters ---------- fname : str Filename to write. Can end with ``.h5`` to write using HDF5. surfs : dict | list of dict The surfaces, or a single surface. %(overwrite)s %(verbose)s rrtrrrTrtrrN) rr0r-rr2r rrrrr_write_bem_surfaces_blockr)rrBrtr$r write_hdf5rr:r:r>r s      r)r$cCs4tt||dgtjgdgd|d}t|||ddS)aWrite a head surface to a fiff file. Parameters ---------- fname : str Filename to write. rr : array, shape (n_vertices, 3) Coordinate points in the MRI coordinate system. tris : ndarray of int, shape (n_tris, 3) Triangulation (each line contains indices for three points which together form a face). %(on_defects)s %(overwrite)s %(verbose)s rrxrF)rrrN)rr0rrr)rrrxrrtr$rr:r:r>write_head_bem)srcCs|D]}t|tjt|tj|dt|tj|dt|tj|dt|tj|dt|tj |dt |tj |dt |tj |ddd |kr|d d k rt|d d krt |tj|d t|tjqd S) z'Write bem surfaces to open file handle.rrrrTrrrxrrNr)rrrrrrrrrrrrrrrErr)rrBrr:r:r>rAs  $rcsRt||dd}|drDt\}}fdddD||ddn t|d S) a@Write a BEM model with solution. Parameters ---------- fname : str The filename to use. Can end with ``.h5`` to write using HDF5. bem : instance of ConductorModel The BEM model with solution to save. %(overwrite)s %(verbose)s See Also -------- read_bem_solution rrrcsi|]}||qSr:r:)r<rurr:r> gsz&write_bem_solution..rTrN)r-rr2_write_bem_solution_fif)rrrtr$rrr:rr>write_bem_solutionSs   rc Cst|dt|}t|tjt|tj|dddt||dd|kr|dtj krht dt|tj tj t |tj|dt|tjW5QRXdS)NrBrrrrz!Only linear collocation supported)rr rrrrrrr rrNrrrrr)rrrr:r:r>rms   rcCstj}t}t|dt|dd}t|}t|}t |sPt d|t ||}t |stt d|f|j |||dt |d}t |d}|||fS) z+Prepare an env object for subprocess calls.rTrz*Could not find the MRI data directory "%s"z.Could not find the subject data directory "%s")SUBJECTrqrumrir) renvironrLr,r*r'rabspath expanduserrrNrCr)rrroZfs_homerrrr:r:r>rs*          rc Csddl}ddlm}t|r&||}t||rg}t|j}|j }|j dkr^|dtj f}t |j dD],}|j|d|f|t|jd} || ql|}~t|dD]@\} } t| r|| } || t|dd|d | d d qdS) Nr) SpatialImager].)affinerrflashmefrZ03drr)rZnibabel.spatialimagesrr4rrrTZ asanyarrayZdataobjrrrdrgr __class__rrrBr|saverrC) rZ flash_echosanglenibrZflash_echo_imgsrrZecho_idxZ this_echo_imgrtZ flash_echor:r:r> _write_echoss2        rc Cs>t||dd\}}t} tt|| d} t|}|d} | d} | jdddd} |rjt|tsjtd |rt|tstd |r t d t t d d dddddddg}|rddg}ndg}d}|D](}|D]}t t d||sd}qq|rVddddddddg}|D]B}|D]6}t t d||stdt d||qq|D]}|D]}t t d||stdt d||tt d||dd}t |dd|d|d}t |rt dnd||g}| || d 7} qbqZn4t|ts$t||dd!t|ts>t||dd!t | d"}tt|}t|dkrrtd#||rt d$|D],}|dd%}d&d'|d(|d)d*g}| |q| dkr| rt| t d+| s| jddd|rt d,|r ttt | d-}tt| dkrRd.g|t| g}| |n t d/t d0| d1sd2d3d4d4| d5| d6| d1g}| || d7n t d8nnt d9|rd-nd:}t| |}t|dkrtd#|d;dam Synthetize the flash 5 files for use with make_flash_bem. This function aims to produce a synthesized flash 5 MRI from multiecho flash (MEF) MRI data. This function can use MEF data with 5 or 30 flip angles. If flash5 (and flash30) images are not explicitly provided, it will assume that the different echos are available in the mri/flash folder of the subject with the following naming convention "mef_.mgz", e.g. "mef05_001.mgz" or "mef30_001.mgz". Parameters ---------- subject : str Subject name. flash30 : bool | list of SpatialImage or path-like | SpatialImage | path-like If False do not use 30-degree flip angle data. The list of flash 5 echos to use. If True it will look for files named mef30_*.mgz in the subject's mri/flash directory and if not False the list of flash 5 echos images will be written to the mri/flash folder with convention mef05_.mgz. If a SpatialImage object each frame of the image will be interpreted as an echo. convert : bool Assume that the Flash MRI images have already been converted to mgz files. DEPRECATED: This option is deprecated and will be removed in 1.2. Set it explicitly to False to silence the deprecation warning and use the flash5_echos and flash30_echos parameters to specify the images to use. unwarp : bool Run grad_unwarp with -unwarp option on each of the converted data sets. It requires FreeSurfer's MATLAB toolbox to be properly installed. %(subjects_dir)s flash5 : list of SpatialImage or path-like | SpatialImage | path-like | True The list of flash 5 echos to use. If True it will look for files named mef05_*.mgz in the subject's mri/flash directory and if not None the list of flash 5 echos images will be written to the mri/flash folder with convention mef05_.mgz. If a SpatialImage object each frame of the image will be interpreted as an echo. %(verbose)s Returns ------- flash5_img : path-like The path the synthesized flash 5 MRI. Notes ----- This function assumes that the Freesurfer segmentation of the subject has been completed. In particular, the T1.mgz and brain.mgz MRI volumes should be, as usual, in the subject's mri directory. Nr^rnrparameter_mapsT)parentsexist_okrz2When passing flash5 images, convert must be False.z3When passing flash30 images, convert must be False.zThe convert parameter is deprecated and will be removed in 1.2. You can now pass the Flash 5 and 30 echos as nibabel images to the function via the flash5_echos and flash30_echosparameters.z" ---- Converting Flash images ----Z001Z002Z003Z004Z005Z006Z007Z008Z05Z30FZ009zDirectory %s is missing.*rrrrzThe file %s is already there mri_convertr)rz mef*_*.mgzz#No suitable source files found (%s)z ---- Unwarp mgz data sets ----zu.mgzZ grad_unwarp-i-oz-unwarptruez! Parameter maps directory clearedz& ---- Creating the parameter maps ----z mef05_*u.mgzZmri_ms_fitparmsz$Parameter maps were already computedz& ---- Synthesizing flash 5 images ---- flash5.mgzZmri_synthesizeZ205T1.mgzzPD.mgzflash5_reg.mgzz+Synthesized flash 5 volume is already therez" ---- Averaging flash5 echoes ----z mef05_*.mgzZ mri_averagez -noconform) missing_ok)rr+rr&rmkdirrboolrr(DeprecationWarningr%rrrrCrNrrrrUrEreplacerrrrlistdirrunlinkr})rZflash30convertZunwarprflash5r$rorrrZ flash_dirZpm_dirZ echos_doneZechosZflashesmissingrZechoZ sample_file dest_filertemplatefilesinfileoutfiler:r:r>convert_flash_mriss8                       r) flash5_imgregisterr$c#Csddlm} t||\} } } t} tt| | d}t| } t| } |dkrV| dd}ntdt|}| d}|j d d d t d ||| df|d }t |rt d |d|dt||g}||nF|dkr| std|dn$t d|ddl}||||rt d|d}| s| d rZ| d}n| d}ddt|dt|dt|g}||n t dn|}t d| d}tj|d d|j d d d d||g}||d }| d}|rt|d!dkrd }d }| d"}|r2t|d!dkr6d }t d#|r| d}|s`td$|j d d d d||g}||n t d%t d&|r| d'}|std(|j d d d d||g}||n t d)t d*d+|g}||~ t d,| d}|j d d d d-d.d/g}|D]T}||d0}t| |d0|t|d d1\}} tt|dd2|| d d3q,t d4| d5|rt|t d6|rt|t d7t|t d8t d9|D]P}| |d2}|s| rd }!n(| r&|t||j ||d }!q|!rZt d:| d}"nt d;| }"t d<|"|r| ||d=dd d>dS)?aCreate 3-Layer BEM model from prepared flash MRI images. Parameters ---------- subject : str Subject name. overwrite : bool Write over existing .surf files in bem folder. show : bool Show surfaces to visually inspect all three BEM surfaces (recommended). %(subjects_dir)s flash_path : str | None [DEPRECATED] Use the flash5_img parameter instead. Path to the flash images. If None (default), mri/flash/parameter_maps within the subject reconstruction is used. .. versionadded:: 0.13.0 .. versionchanged:: 1.1 Deprecated copy : bool If True (default), use copies instead of symlinks for surfaces (if they do not already exist). .. versionadded:: 0.18 .. versionchanged:: 1.1 Use copies instead of symlinks. flash5_img : None | path-like | Nifti1Image The path to the synthesized flash 5 MRI image or the image itself. If None (default), the path defaults to flash5.mgz within the flash_path folder. If not present the image is copied or written to the flash_path folder as flash5.mgz. .. versionadded:: 1.1.0 register : bool Register the flash 5 image with T1.mgz file. If False, we assume that the images are already coregistered. .. versionadded:: 1.1.0 %(verbose)s See Also -------- convert_flash_mris Notes ----- This program assumes that FreeSurfer is installed and sourced properly. This function extracts the BEM surfaces (outer skull, inner skull, and outer skin) from a FLASH 5 MRI image synthesized from multiecho FLASH images acquired with spin angles of 5 and 30 degrees. rrlrnNrrzpThe flash_path parameter is deprecated and will be removed in version 1.1. Use the flash5_img parameter instead.rqT)rrz Processing the flash MRI data to produce BEM meshes with the following parameters: SUBJECTS_DIR = %s SUBJECT = %s Result dir = %s rzCopying flash 5 image z to rz!Flash 5 image cannot be found at .zWriting flash 5 image at rz- ---- Registering flash 5 with T1 MPRAGE ----rrrjZfsl_rigid_registerz-rrrz)Registered flash 5 image is already therez3 ---- Converting flash5 volume into COR format ----r) ignore_errorsFzCOR*rwz/ ---- Converting T1 volume into COR format ----z'Both T1 mgz and T1 COR volumes missing.z"T1 volume is already in COR formatz2 ---- Converting brain volume into COR format ----z brain.mgzz-Both brain mgz and brain COR volumes missing.z%Brain volume is already in COR formatz$ ---- Creating the BEM surfaces ----Zmri_make_bem_surfacesz3 ---- Converting the tri files into surf files ----rrr z.tri)Zswapz.surfrz ---- Cleaning up ----zinner_skull_tmp.trizDeleted the T1 COR volumezDeleted the brain COR volumezDeleted the flash5 COR volumez" ---- Creating symbolic links ----ryrzz Thank you for waiting. The BEM triangulations for this subject are now available at: %s. We hope the BEM meshes created will facilitate your MEG and EEG data analyses.r{r|)!r~rmrr+rr&rr(resolverr%rr4rrrrrrris_dirnextris_filerNmoverrrsplitextrrr)#rrtr}rZ flash_pathrLrrr$rmrorrrrrrrZ flash5_regZ ref_volumeZ flash5_dirZ convert_T1rZ convert_brainZ brain_dirZT1_fnameZ brain_fnameZ flash_bem_dirrBrZ out_fnamerrxrrr:r:r>make_flash_bemds7                                         rcCs4t|dkr0|dddkr0td|dddS)zCheck bem surface sizes.rrrTi'ztThe bem surfaces have %s data points. 5120 (ico grade=4) should be enough. Dense 3-layer bems may not save properly.N)rEr(rr:r:r>r1s rcCs`|sLt|t|}zt||Wn$tk rJtd|d}YnX|r\t||dS)z)Create a relative symlink (or just copy).zuCould not create symbolic link %s. Check that your partition handles symbolic links. The file will be copied instead.TN) rrelpathdirnamersymlinkOSErrorr(rrL)srcrrLZsrc_linkr:r:r>r9s rr:rc Cs*tdd|Dstdtf|}t|||t|trdtdt|dt |}t d|d}n4t|trt |D] \}}t|t |d|d qvt|trt d|d}t|t r&|d r&| }g|d <t|d d kr&t tD]2\}}|d t||d dd||d dd<q|S)Ncss|]}|dtfkVqdSr)r5)r<rIr:r:r>r?Lsz'_ensure_bem_surfaces..z path-likezLoading BEM surfaces from rF)r6rB[]r6rBrAr)ZcompleterMr)rr}rr*rr0r%rrrr5r|r0rLrErvaluesrBr)rZ extra_allowrallowedii this_surfrtrr:r:r>rHs2       rcCs"t|r|std|ddS)zPrevent overwrites.zFile z( exists, use --overwrite to overwrite itN)rrIOError)rrtr:r:r> _check_filefsri0ui )Zmediumsparserr) thresholdrr$c Cst|dd}|rdnd}t||} t| s:td| t|td|dkrjtt| d|rf|nd}td t| d fd d } | } t |d }| dkrt t j } || d<|| d<|d|| d<d| krtdt dd|d|dt|dt|g | d| } | dkrtdt||d}t|s>t |t|d|}|d}td|t||d }t| gtjgd!g||d"d#} t|| |d$t d%d&d'krt| d(g}ttd)D]\}\}}|rqt|d*|d+t|d,t| d(d-|d.t| d/| d(|d0\}}||}td1||ft||tt||d2gtjgd!gd3||d4}t|||d$qtd5dS)6aCreate surfaces of the scalp and neck. The scalp surfaces are required for using the MNE coregistration GUI, and allow for a visualization of the alignment between anatomy and channel locations. Parameters ---------- %(subject)s %(subjects_dir)s force : bool Force creation of the surface even if it has some topological defects. Defaults to ``True``. See :ref:`tut-fix-meshes` for ideas on how to fix problematic meshes. %(overwrite)s no_decimate : bool Disable the "medium" and "sparse" decimations. In this case, only a "dense" surface will be generated. Defaults to ``False``, i.e., create surfaces for all three types of decimations. threshold : int The threshold to use with the MRI in the call to ``mkheadsurf``. The default is 20. .. versionadded:: 1.1 mri : str The MRI to use. Should exist in ``$SUBJECTS_DIR/$SUBJECT/mri``. .. versionadded:: 1.1 %(verbose)s Trr(rz<%s does not exist. Please check your subject directory path.rrrjz91. Creating a dense scalp tessellation with mkheadsurf...rcSs0d}dD]"}t||}t|r|}q,q|S)N)z lh.segheadz lh.smseghead)rrCr)Z surf_pathrrurr:r:r> check_segheads  z*make_scalp_surfaces..check_segheadrNrqr/ZsubjdirruztThe FreeSurfer environment needs to be set up to use make_scalp_surfaces to create the outer skin surface lh.segheadZ mkheadsurfz-subjidz-srcvolz-thresh1z-thresh2)roz4mkheadsurf did not produce the standard output file.rz%s-head-{}.fifZdensez2. Creating %s ...zV Consider using pymeshfix directly to fix the mesh, or --force to ignore the problem.r)rrIrrZ_MNE_TESTING_SCALPfalserrxr]z . Creating z tessellation...z&.1 Decimating the dense tessellation (z -> z triangles)...r)rbZ trianglesZ n_trianglesz%i.2 Creating %srF)rrrIr)r'rrCrrNr*rr%rr3rrrr&rrrrrrrrgetenvrEr| _tri_levelsitemsr r0)rrforcertZ no_decimaterrr$rZ subj_pathrZ my_segheadZthis_envrrZfname_templateZ dense_fnamerrxrrerrbZ dec_fnameZdec_surfr:r:r>make_scalp_surfacesrs"               $    r%c Cs|j}|dkr |tjddf}|jd}t|f}td|dt|d|dr|d}|rvt||d d }|d dd }t |tj j ||dd }n4|ddd} |rt|| d d } t | |d d\} }|dkr|d}|S)a7Calculate the distance of positions to inner skull surface. Parameters ---------- pos : array, shape (..., 3) Position(s) in m, in head coordinates. bem : instance of ConductorModel Conductor model. %(trans)s If None (default), assumes bem is in head coordinates. %(verbose)s Returns ------- distances : float | array, shape (...) The computed distance(s). A float is returned if pos is an array of shape (3,) corresponding to a single position. Notes ----- .. versionadded:: 1.1 rNrz.Computing distance to inner skull surface for z positionrr6r@T)r rArHr_rBrr) rrTrdrrcr%rr)r"rerUrVr) posrZtransr$rrZdistancerGrDZsurface_pointsrr:r:r>distance_to_bems<    r')Frr)N)r)r)NTrr)rrNN)r5r6Nr7r8N)r;r N)r;TN)N)r;)r[F) NFrjFFNFTNrkN)FNrN)N)N)FN)rF)FN)TTFNTN)FTNNT)F)r:r)NTFF)NN) collectionsr functoolsrrros.pathpathrpathlibrrrLrnumpyrTZ io.constantsrr Zio._digitizationr r r Zio.writer rrrrrrZio.tagrZio.treerZio.openrZsurfacerrrrrrrrrr Z transformsr!r"r#utilsr$r%r&r'r(r)r*r+r,r-r.r/r0r1r2r3r4r0r5r\rwrrrrrrrrrrrrrrrrrr rrr!r"r4rFr@rTrHr]rirrrrrrrrrrZFIFFV_BEM_SURF_ID_CSFrrrrrrrrrrrrrrrrrrrrrr"r%r'r:r:r:r> sV     $   0L 5(  ,%      * C# * r & G    ( , % E M    .M  r