U f{je@sdZddlmZddlZddlmZddlm Z m Z ddl m Z ddl mZddlmZmZmZmZmZmZdd lmZmZdd lmZmZmZmZmZmZm Z d d Z!d dZ"d?ddZ#d@ddZ$ddZ%ddZ&ddZ'ddZ(dAddZ)edBd d!Z*edCd"d#Z+edDd$d%Z,edEd&d'Z-edFd(d)Z.d*d+Z/edGd,d-Z0edHd.d/Z1d0d1Z2dId3d4Z3dJd5d6Z4dKd7d8Z5edLd9d:Z6edMd;d<Z7d=d>Z8dS)NzFreesurfer handling functions.N)GzipFile)_bem_find_surfaceread_bem_surfaces)FIFF)read_fiducials) apply_transinvert_transformcombine_transforms _ensure_transread_ras_mni_t Transform) read_surface_read_mri_surface)verbose_validate_type _check_fname _check_optionget_subjects_dir_require_versionloggerc CsTt|dd}dD]6}tt||d|dstdt||qt||S)z;Check that the Freesurfer subject directory is as expected.TZ raise_error)ZT1brainasegmri.mgzzNFreesurfer recon-all subject folder is incorrect or improperly formatted, got )ropisfilejoin ValueError)subject subjects_dirZimg_namer"N/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/_freesurfer.py_check_subject_dirs r$cCsttdddddl}t|dd}|ds8td |tt||d |d d dd }||}t |j }||fS)z?Check that the anatomical segmentation file exists and load it.nibabelz load asegz2.1.0rNTrrz+`aseg` file path must end with "aseg", got rrread) overwrite must_exist) rr%rendswith RuntimeErrorrrrloadnparraydataobj)rr r!nibZ aseg_datar"r"r# _get_aseg"s     r0 use MRI filesc CsPz ddl}Wn.tk r:}zd||f}W5d}~XYnXd}|rLt||S)Nrz"nibabel is required to %s, got: %s)r% ImportError)whyr/expmsgr"r"r#_import_nibabel1s r7RASc Csddl}t|jtj}|j|j|j t }|j|}|j ||}|j ||}| ||j }|j||j} t|j| } || fS)aReorient an image to a given orientation. Parameters ---------- img : instance of SpatialImage The MRI image. axcodes : tuple | str The axis codes specifying the orientation, e.g. "RAS". See :func:`nibabel.orientations.aff2axcodes`. Returns ------- img_data : ndarray The reoriented image data. vox_ras_t : ndarray The new transform from the new voxels to surface RAS. Notes ----- .. versionadded:: 0.24 rN)r%r,r-r.astypefloat32Z orientationsZ axcodes2orntZ aff2axcodesaffineintZornt_transformZapply_orientationMGHImageZ inv_ornt_affshapedotheaderget_vox2ras_tkr) ZimgZaxcodesr/Z orig_dataZorntZras_orntZ ornt_transZimg_dataZorig_mghZ aff_trans vox_ras_tr"r"r#_reorient_image=s  rCcCsJtd|dtdddd|}ttdddgt|g\}}|||fS)aGet MRI orientation information from an image. Parameters ---------- orientation : str Orientation that you want. Can be "axial", "sagittal", or "coronal". Returns ------- axis : int The dimension of the axis to take slices over when plotting. x : int The dimension of the x axis. y : int The dimension of the y axis. Notes ----- .. versionadded:: 0.21 .. versionchanged:: 0.24 orientation)ZcoronalZaxialZsagittalrr)rdictsortedset difference)rDZaxisxyr"r"r#_mri_orientationas "rLcCs|r tdt}t|dd\}|d<|d<}}}|j|d|d|d|d|r|dk s`tt|d|d <t|j|d <|S) Nzload MRI atlas dataT) return_img vox_mri_t mri_ras_trr)Z mri_widthZ mri_heightZ mri_depthZmri_volume_name mri_vox_tdata) r7rF_read_mri_infoupdateAssertionErrorr r,asarrayr.)rrQout_dimsZmgzr"r"r#_get_mri_info_data}s$ rYc Cst|dddd}|ds"tdddd d d d d dg}t|}t|d}||j}W5QRXtjd||d}|d t }t |dkr|ddn|}|d}t |t }t ||d} tj |d dd| dgdd|d| d gd|d d| dgddddggtjd} t|} |d} |dj} |dt| t| | }tdd}t| | |ddddf<|j|dddf<t|| ||dd}|S)z4Adapted from nibabel to quickly extract header info.r&Tz MRI imager'r(namerzFilename must end with .mgz)version>i4)rXr]))typer])Zdofr])Z goodRASFlagz>i2)delta>f4)Mdcra)rcrc)Pxyz_crarbrbr")r>dtypebufferrXr^Nrcr`g@rrErrgrdre)rX vox2ras_tkrvox2raszooms)rr)IOErrorr,rgrr&itemsizendarrayr9r<lenr-floatr:ZdiagTr?eyerF)fnameZ header_dtdZ header_dtypefidZhdr_strr@rXr`ZdsnsZv2rtkrdZpcrs_crdZpxyz_0Mr"r"r#_get_mgz_headersT        rycCszt|d|}|dk|t|djtdk@d}t||jtj }t |jdtj }|dt |||<|S)NrPgrQ?r) rr,r-r>r<allroundrrr9Zint64fullnantuple)Zvol_inforrZrr_voxZgoodidxvaluesr"r"r#_get_atlas_valuessrFc sddl}t|std|||}t|j}t|}dkrRt \n |r^t dt t |tfddtDfddd }|rfd d |D|f}n|}|S) aReturn a list of names and colors of segmented volumes. Parameters ---------- mgz_fname : str Filename to read. Typically aseg.mgz or some variant in the freesurfer pipeline. return_colors : bool If True returns also the labels colors. atlas_ids : dict | None A lookup table providing a mapping from region names (str) to ID values (int). Can be None to use the standard Freesurfer LUT. .. versionadded:: 0.21.0 Returns ------- label_names : list of str The names of segmented volumes included in this mgz file. label_colors : list of str The RGB colors of the labels included in this mgz file. See Also -------- read_freesurfer_lut Notes ----- .. versionchanged:: 0.21.0 The label names are now sorted in the same order as their corresponding values in the MRI file. .. versionadded:: 0.9.0 rNzaseg file "%s" not foundz5return_colors must be False if atlas_ids are providedc3s|]\}}|r|VqdSNr").0Zkikey)keepr"r# sz.get_volume_labels_from_aseg..cs|Srr")rJ) atlas_idsr"r#z-get_volume_labels_from_aseg..)rcsg|] }|qSr"r")rk)colorsr"r# sz/get_volume_labels_from_aseg..)r%rrrmr+r,rUr.uniqueread_freesurfer_lutrZin1dlistrrG enumeratekeys) Z mgz_fnameZ return_colorsrr/ZatlasrQZwantrrVr")rrrr#get_volume_labels_from_asegs&$        rc CsVt|dd}t||dd}t|dd}t|\}}}}}t||dd} dt| |S)a:Convert pos from head coordinate system to MRI ones. This function converts to MRI RAS coordinates and not to surface RAS. Parameters ---------- pos : array, shape (n_pos, 3) The coordinates (in m) in head coordinate system. %(subject)s mri_head_t : instance of Transform MRI<->Head coordinate transformation. %(subjects_dir)s %(verbose)s Returns ------- coordinates : array, shape (n_pos, 3) The MRI RAS coordinates (in mm) of pos. Notes ----- This function requires nibabel. TrrT1.mgzheadras@@)rrrr rRr r) posr mri_head_tr!rZt1_fnameZ head_mri_trWrOZ head_ras_tr"r"r# head_to_mris   rc sd}t|ts$t|tjs$d}|g}t|tsHt|tjsH|gt|}t|t|ks`tdtddfdddD}dd|Dt}|d d d d fd 9<tfd dt ||D}|r|d}t |d |S)aConvert the array of vertices for a hemisphere to MNI coordinates. Parameters ---------- vertices : int, or list of int Vertex number(s) to convert. hemis : int, or list of int Hemisphere(s) the vertices belong to. %(subject)s subjects_dir : str, or None Path to SUBJECTS_DIR if it is not set in the environment. %(verbose)s Returns ------- coordinates : array, shape (n_vertices, 3) The MNI coordinates (in mm) of the vertices. FTz&hemi and vertices must match in lengthrc s g|]}tdd|qS)surfz%s.white)rr)rh)r r!r"r#rFsz!vertex_to_mni..)ZlhZrhcSsg|]}t|dqSr)r)rsr"r"r#rJstransNrcrcs$g|]\}}||ddfqSrr")rrv)rr"r#rOsr) isinstancerr,rorprr read_talxfmr-zipr) ZverticesZhemisr r!rZ singletonZsurfsxfmrQr")rr r!r# vertex_to_mni%s&   rcCs6t|dd}tt|ddt||dd}t||dS)aConvert pos from head coordinate system to MNI ones. Parameters ---------- pos : array, shape (n_pos, 3) The coordinates (in m) in head coordinate system. %(subject)s mri_head_t : instance of Transform MRI<->Head coordinate transformation. %(subjects_dir)s %(verbose)s Returns ------- coordinates : array, shape (n_pos, 3) The MNI coordinates (in mm) of pos. Notes ----- This function requires either nibabel. Trrrmni_talr)rr r rr)rr rr!rZ head_mni_tr"r"r# head_to_mniXs  rcCsjtttddd}t|\}}|tjks0t|dkr<|Stt ||}|D]}t ||d|d<qN|S)uEstimate fiducials for a subject. Parameters ---------- %(subject)s %(subjects_dir)s %(verbose)s Returns ------- fids_mri : list List of estimated fiducials (each point in a dict), in the order LPA, nasion, RPA. Notes ----- This takes the ``fsaverage-fiducials.fif`` file included with MNE—which contain the LPA, nasion, and RPA for the ``fsaverage`` subject—and transforms them to the given FreeSurfer subject's MRI space. The MRI of ``fsaverage`` is already in MNI Talairach space, so applying the inverse of the given subject's MNI Talairach affine transformation (``$SUBJECTS_DIR/$SUBJECT/mri/transforms/talairach.xfm``) is used to estimate the subject's fiducial locations. For more details about the coordinate systems and transformations involved, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and :ref:`tut-source-alignment`. rQZ fsaveragezfsaverage-fiducials.fifr) rrdirname__file__rrZFIFFV_COORD_MRIrTr rr)r r!rZ fname_fids_fsZfids coord_frameZ mni_mri_tfr"r"r#get_mni_fiducialsys" rc CsTddlm}m}t|dd}t||\}}}||d|d|ddd}t||S)aEstimate the head->mri transform from fsaverage fiducials. A subject's fiducials can be estimated given a Freesurfer ``recon-all`` by transforming ``fsaverage`` fiducials using the inverse Talairach transform, see :func:`mne.coreg.get_mni_fiducials`. Parameters ---------- %(subject)s %(subjects_dir)s %(verbose)s Returns ------- %(trans_not_none)s r)make_dig_montagecompute_native_head_tTrrr)lpanasionrpar)Zchannels.montagerrrrr ) r r!rrrrrrZmontager"r"r#estimate_head_mri_ts rcCsnddl}t||jjs ||}||jtj |j }|t ||dd}tj |j |j ddsjtd|S)z6Check if the image is in Freesurfer surface RAS space.rNrz brain.mgzgư>)ZatolzThe `image` is not aligned to Freesurfer surface RAS space. This space is required as it is the space where the anatomical segmentation and reconstructed surfaces are)r%rZ spatialimagesZ SpatialImager+r=r.r9r,r:r;rrZallcloser*)imager r!r/Zfs_imgr"r"r#_ensure_image_in_surface_RASs rc CsJt|ddt|dddt|d}t|dd}W5QRX|S) aRead a Freesurfer linear transform array file. Parameters ---------- fname : str | None The transform filename. %(verbose)s Returns ------- affine : ndarray The affine transformation described by the lta file.  path-likeNrtr&Tr(r )rropenr,Zloadtxt readlines)rtrrur;r"r"r#read_ltas    rcCst|}t||}|ddddfd<t||dd}t|sXt||dd}t|sntd|t|\}}}}}t||dd }|S) a!Compute MRI-to-MNI transform from FreeSurfer talairach.xfm file. Parameters ---------- %(subject)s %(subjects_dir)s %(verbose)s Returns ------- mri_mni_t : instance of Transform The affine transformation from MRI to MNI space for the subject. rNrcrrzorig.mgzrzmri not found: %sr)rr rrrrmrRr )r r!rZ ras_mni_tpathrWrOZ mri_mni_tr"r"r#rs    rcCst|ddt|r(t||kr(|St|s|dkrJtd|dt|dd}t||d|}t|std|dt||krd |d }t||S) z@Check whether an mri exists in the Freesurfer subject directory.rrNz MRI file z" not found and no subject providedTrz not foundzAmbiguous filename - found zQ in current folder. If this is correct prefix name with relative or absolute path)rrrbasenameFileNotFoundErrorrrrm)rr r!errr"r"r# _check_mris       rmcCs,|rBddl}||j}|}|}|}|dd} n(t|}|d}|d}|d}|d} tdd|} tdd |} t t | | d d} |d kst |d krt d d d d ggj} | d| 9<| d| 9<| dddddf| 9<| | | || f}|r(t}|||f7}|S)NrrcrkrjrXrlZ mri_voxelrr)rmmrgMbP?rrr^)r%r+r@Z get_vox2rasrAZget_data_shapeZ get_zoomsryr r r rTr,r-rrr7)rZunitsrMZ use_nibabelr%hdrZn_origZt_origrXrlrBrNrOconvrVr"r"r#rR"s>     rRcCsdt|}|d|d}}t|d|d|d|dgtj}tt||}tt||}||fS)a7Read a Freesurfer-formatted LUT. Parameters ---------- fname : str | None The filename. Can be None to read the standard Freesurfer LUT. Returns ------- atlas_ids : dict Mapping from label names to IDs. colors : dict Mapping from label names to colors. r[idRGBA)_get_lutr,r-rqrrrFr)rtlutnamesZidsrrr"r"r#rMs &rc st|dd|dkr(tttdd}t|dddd d d d d dg}dd|Dt|dt}|D]h}|}|dsd|sqd| }t |t |krt d|t ||D]\}}|d |qqdW5QRXfdd|Dt ddkstS)zGet a FreeSurfer LUT.rrtNrQzFreeSurferColorLUT.txtr&Tr)rmsz_get_lut..r#zLUT is improperly formatted: rcs,i|]$}|dtj|d|ddqS)rrri)r,r-rrr"r#rxsr[)rrrrrrrstrip startswithsplitrpr*rappendrT)rtrgrulinerwpartr"rr#rds4   rc Csdtd|d|dkrH|dk rHz t|dWStk rFtdYnX|dkrd|dkr\dStdtt|d d |}|d krt|d |d t|ddg}nBt|d dt|d ddt|d |dt|d |dg}|D]Z}t |rtdt |dt |ddkr8t |dddSt |Sqtd|dd|dS)aGet a head surface from the Freesurfer subject directory. Parameters ---------- surf : str The name of the surface 'auto', 'head', 'outer_skin', 'head-dense' or 'seghead'. %(subject)s %(subjects_dir)s bem : mne.bem.ConductorModel | None The conductor model that stores information about the head surface. %(verbose)s Returns ------- head_surf : dict | None A dictionary with keys 'rr', 'tris', 'ntri', 'use_tris', 'np' and 'coord_frame' that store information for mesh plotting and other useful information about the head surface. Notes ----- .. versionadded: 0.24 r)autor outer_skin head-denseseghead)rrrNrz`Could not find the surface for head in the provided BEM model, looking in the subject directory.rzsTo plot the head surface, the BEM/sphere model must contain a head surface or "subject" must be provided (got None)Tr)rrbemz-head-dense.fifz lh.segheadzouter_skin.surfZflashz-head-sparse.fifz -head.fifzUsing z for head surface.r{z.fifwarn)Z on_defectsrz"No head surface found for subject z after trying:  )rrr*rinforrrrexistsrsplitextrrrm)rr r!rrZ subject_dirZ try_fnamesrtr"r"r#_get_head_surface}sJ      rcCsr|dk r8zt||dWStk r6tdYnXt|dd}tt||d|ddd|d d }t|S) avGet a skull surface from the Freesurfer subject directory. Parameters ---------- surf : str The name of the surface 'outer' or 'inner'. %(subject)s %(subjects_dir)s bem : mne.bem.ConductorModel | None The conductor model that stores information about the skull surface. %(verbose)s Returns ------- skull_surf : dict | None A dictionary with keys 'rr', 'tris', 'ntri', 'use_tris', 'np' and 'coord_frame' that store information for mesh plotting and other useful information about the head surface. Notes ----- .. versionadded: 0.24 NZ_skullzaCould not find the surface for skull in the provided BEM model, looking in the subject directory.Trrz _skull.surfr&z skull surfacerZ) rr*rrrrrrr)rr r!rrrtr"r"r#_get_skull_surfaces  rc Cs|ddlm}m}t||}ttdddddftddg}tt||}|||ddd}|d|dd }|S) Nr)fit_matched_points_trans_from_paramsr^rcrzparams)scalerV)TTF) Zcoregrrrr,Z concatenatersrr ) r r!rrrZpts_talZpts_subjrZrigidr"r"r#_estimate_talxfm_rigids .r)r1)r8)FN)NN)NN)NN)NN)NN)N)NN)rFF)N)N)NN)NN)9__doc__os.pathrrnumpyr,gziprrrrZ io.constantsrZ io.meas_inforZ transformsrr r r r r Zsurfacerrutilsrrrrrrrr$r0r7rCrLrYryrrrrrrrrrrrrRrrrrrr"r"r"r#s`     $  $'  ? % 2  /   % +   A '