text: Search.setIndex({docnames:["brainload","braintools","index","workflows"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,sphinx:55},filenames:["brainload.rst","braintools.rst","index.rst","workflows.rst"],objects:{"":{brainload:[0,0,0,"-"]},"brainload.annotations":{AnnotQuery:[0,2,1,""],annot:[0,1,1,""],color_rgbt_to_rgba:[0,1,1,""],get_atlas_region_names:[0,1,1,""],get_atlas_region_names_hardcoded:[0,1,1,""],label:[0,1,1,""],label_to_mask:[0,1,1,""],mask_data_using_label:[0,1,1,""],read_annotation_md:[0,1,1,""],read_label_md:[0,1,1,""],read_vertex_list_file:[0,1,1,""],region_data_native:[0,1,1,""],region_stats:[0,1,1,""],vertices_to_label:[0,1,1,""]},"brainload.annotations.AnnotQuery":{compute_labels:[0,3,1,""],get_vertex_label_colors:[0,3,1,""],get_vertex_label_names:[0,3,1,""]},"brainload.braindescriptors":{BrainDescriptors:[0,2,1,""]},"brainload.braindescriptors.BrainDescriptors":{add_curv_stats:[0,3,1,""],add_custom_measure_stats:[0,3,1,""],add_parcellation_stats:[0,3,1,""],add_segmentation_stats:[0,3,1,""],add_single_segmentation_stats:[0,3,1,""],add_standard_stats:[0,3,1,""],check_for_NaNs:[0,3,1,""],check_for_curv_stats_files:[0,3,1,""],check_for_custom_measure_stats_files:[0,3,1,""],check_for_hemi_dependent_file:[0,3,1,""],check_for_hemi_independent_file:[0,3,1,""],check_for_parcellation_stats_files:[0,3,1,""],check_for_segmentation_stats_files:[0,3,1,""],report_descriptors:[0,3,1,""],save:[0,3,1,""]},"brainload.brainlocate":{BrainLocate:[0,2,1,""]},"brainload.brainlocate.BrainLocate":{get_closest_vertex:[0,3,1,""],get_closest_vertex_and_distance:[0,3,1,""]},"brainload.brainvoxlocate":{BrainVoxLocate:[0,2,1,""]},"brainload.brainvoxlocate.BrainVoxLocate":{get_closest_not_unknown:[0,3,1,""],get_ras_coords_at_voxel_crs:[0,3,1,""],get_voxel_crs_at_ras_coords:[0,3,1,""],get_voxel_segmentation_labels:[0,3,1,""]},"brainload.brainwrite":{get_surface_vertices_overlay_text_file_lines:[0,1,1,""],get_surface_vertices_overlay_volume_data:[0,1,1,""],get_surface_vertices_overlay_volume_data_1color:[0,1,1,""],get_volume_data_with_custom_marks:[0,1,1,""],write_voldata_to_mgh_file:[0,1,1,""],write_voldata_to_nifti_file:[0,1,1,""]},"brainload.freesurferdata":{fsaverage_mesh:[0,1,1,""],get_morphometry_file_path:[0,1,1,""],get_num_fsaverage_verts_per_hemi:[0,1,1,""],get_standard_space_morphometry_file_path:[0,1,1,""],get_surface_file_path:[0,1,1,""],get_vox2ras_and_ras2vox_from_nifti_file:[0,1,1,""],group:[0,1,1,""],group_native:[0,1,1,""],hemi_range:[0,1,1,""],load_subject_mesh_files:[0,1,1,""],load_subject_morphometry_data_files:[0,1,1,""],merge_morphometry_data:[0,1,1,""],parse_talairach_file:[0,1,1,""],read_fs_morphometry_data_file_and_record_meta_data:[0,1,1,""],read_fs_surface_file_and_record_meta_data:[0,1,1,""],read_lookup_file:[0,1,1,""],read_m3z_file:[0,1,1,""],read_mgh_file:[0,1,1,""],read_mgh_header_matrices:[0,1,1,""],rhi:[0,1,1,""],rhv:[0,1,1,""],subject:[0,1,1,""],subject_avg:[0,1,1,""],subject_data_native:[0,1,1,""],subject_data_standard:[0,1,1,""],subject_mesh:[0,1,1,""]},"brainload.meshexport":{mesh_to_obj:[0,1,1,""],mesh_to_ply:[0,1,1,""],scalars_to_colors_clist:[0,1,1,""],scalars_to_colors_matplotlib:[0,1,1,""]},"brainload.nitools":{detect_subjects_in_directory:[0,1,1,""],do_subject_files_exist:[0,1,1,""],fill_template_filename:[0,1,1,""],load_vertex_indices:[0,1,1,""],load_voxel_indices:[0,1,1,""],read_BIDS_participants_file:[0,1,1,""],read_subjects_file:[0,1,1,""],save_vertex_indices:[0,1,1,""],write_BIDS_participants_file:[0,1,1,""],write_lines_to_text_file:[0,1,1,""],write_subjects_file:[0,1,1,""]},"brainload.spatial":{apply_affine:[0,1,1,""],apply_affine_3D:[0,1,1,""],coords_a2s:[0,1,1,""],coords_s2a:[0,1,1,""],deg2rad:[0,1,1,""],get_affine_matrix_MNI152_to_MNI305:[0,1,1,""],get_affine_matrix_MNI305_to_MNI152:[0,1,1,""],get_equivalent_voxel_of_raw_volume_in_conformed_volume:[0,1,1,""],get_freesurfer_matrix_ras2vox:[0,1,1,""],get_freesurfer_matrix_vox2ras:[0,1,1,""],get_n_neighborhood_indices_3D:[0,1,1,""],get_n_neighborhood_indices_3D_points:[0,1,1,""],get_n_neighborhood_start_stop_indices_3D:[0,1,1,""],get_n_neighborhood_start_stop_indices_3D_points:[0,1,1,""],mirror_3D_coordinates_at_axis:[0,1,1,""],parse_registration_matrix:[0,1,1,""],point_mirror_3D_coordinates:[0,1,1,""],rad2deg:[0,1,1,""],rotate_3D_coordinates_around_axes:[0,1,1,""],scale_3D_coordinates:[0,1,1,""],translate_3D_coordinates_along_axes:[0,1,1,""]},"brainload.stats":{extract_column_from_table_data:[0,1,1,""],extract_field_from_table_data:[0,1,1,""],extract_table_data_indices_where:[0,1,1,""],get_stats_table_column_names:[0,1,1,""],group_stats:[0,1,1,""],group_stats_aparc:[0,1,1,""],group_stats_aparc_DKTatlas:[0,1,1,""],group_stats_aparc_a2009s:[0,1,1,""],group_stats_aseg:[0,1,1,""],group_stats_by_row:[0,1,1,""],measures_to_numpy:[0,1,1,""],parse_curve_stats:[0,1,1,""],parse_curve_stats_file:[0,1,1,""],register_dat_matrix:[0,1,1,""],stat:[0,1,1,""],stats_table_region_label_column_name:[0,1,1,""],stats_table_to_numpy:[0,1,1,""],stats_table_to_numpy_by_row:[0,1,1,""],typelist_for_aparc_atlas_stats:[0,1,1,""],typelist_for_aseg_stats:[0,1,1,""]},"brainload.surfacegraph":{SurfaceGraph:[0,2,1,""]},"brainload.surfacegraph.SurfaceGraph":{get_neighbors_up_to_dist:[0,3,1,""]},brainload:{annot:[0,1,1,""],annotations:[0,0,0,"-"],braindescriptors:[0,0,0,"-"],brainlocate:[0,0,0,"-"],brainvoxlocate:[0,0,0,"-"],brainwrite:[0,0,0,"-"],detect_subjects_in_directory:[0,1,1,""],freesurferdata:[0,0,0,"-"],fsaverage_mesh:[0,1,1,""],group:[0,1,1,""],group_native:[0,1,1,""],hemi_range:[0,1,1,""],label:[0,1,1,""],mesh_to_obj:[0,1,1,""],mesh_to_ply:[0,1,1,""],meshexport:[0,0,0,"-"],nitools:[0,0,0,"-"],read_subjects_file:[0,1,1,""],rhi:[0,1,1,""],rhv:[0,1,1,""],spatial:[0,0,0,"-"],stat:[0,1,1,""],stats:[0,0,0,"-"],subject:[0,1,1,""],subject_avg:[0,1,1,""],subject_data_native:[0,1,1,""],subject_data_standard:[0,1,1,""],subject_mesh:[0,1,1,""],surfacegraph:[0,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","class","Python class"],"3":["py","method","Python method"]},objtypes:{"0":"py:module","1":"py:function","2":"py:class","3":"py:method"},terms:{"1mm":0,"2009s":0,"201x201x201":0,"20explain":0,"256x256x256":0,"2mm":0,"3x1":0,"3x3":0,"4x4":0,"7x7x7":0,"boolean":0,"byte":0,"case":[0,3],"class":0,"default":[0,3],"export":0,"float":0,"function":[0,1,3],"import":[0,3],"int":0,"long":0,"new":0,"return":[0,3],"short":0,"true":0,"try":[0,3],And:0,But:0,CRS:0,For:0,Has:0,IDs:0,Its:0,NOT:0,One:0,RAS:0,RCS:0,Raed:[],Such:0,That:[0,3],The:[0,3],Then:0,There:0,These:0,Use:0,Useful:0,Uses:0,Using:0,Will:0,With:0,Yes:0,_hardcoded_text:0,_hemi_:0,a2009:[0,3],about:0,abov:0,absolut:0,abus:0,access:[0,1],accord:0,actual:[0,3],add:0,add_curv_stat:0,add_custom_measure_stat:0,add_parcellation_stat:0,add_segmentation_stat:0,add_single_segmentation_stat:0,add_standard_stat:0,added:0,advanc:0,affin:0,affine_matrix:0,after:0,algorithm:0,all:[0,1,3],all_subjects_data:0,all_subjects_measures_dict:0,all_subjects_table_data:0,all_subjects_table_data_dict:0,all_subjects_table_data_dict_by_region:0,all_vert_coord:0,allow:0,almost:0,along:0,alpha:0,alreadi:[0,3],also:[0,3],alsononstandard:0,alter:0,altern:0,alwai:[0,3],ampersand:0,amygdala:0,analysi:[0,3],anatom:0,angl:0,ani:0,annot:[2,3],annot_list:0,annotation_fil:0,annotqueri:0,anoth:0,answer:0,anterior:0,aparc:[0,3],aparcstats2t:0,api:[2,3],appli:0,applic:0,apply_affin:0,apply_affine_3d:0,appropri:0,approxim:0,arbitrari:0,area:[0,3],argument:0,around:0,arrai:0,articl:0,ascii:0,aseg:0,asg:0,asgeg:0,ask:0,assert:0,assign:[0,3],associ:0,assum:[0,3],atla:[0,2],atlas:0,atlas_list:0,auto:0,automat:0,avail:[0,2,3],averag:[0,3],average_subject:0,avg:0,avoid:0,awai:0,axes:0,axi:0,axial:0,back:0,background:0,background_rgb:0,background_valu:0,background_voxel_valu:0,banksst:3,base:[0,3],basi:0,basic:0,becaus:0,becom:0,been:[0,2],befor:0,beforehand:0,being:0,belong:0,below:0,bert:[0,3],best:0,better:0,between:0,bid:0,binari:0,bioelectromagnet:0,bit:0,blob:0,blue:0,bool:0,border:0,both:0,both_hemis_morphometry_data:0,bottom:0,brain:[0,1,2],brain_mesh_info:1,brain_morph_info:1,brain_qa:1,brain_vol_info:1,braindescriptor:2,brainloc:2,brainvoxloc:2,brainwrit:2,brett:0,bright:0,bring:0,built:1,call:0,cam:0,can:[0,1,3],cannot:0,care:0,cast:0,cbu:0,center1:0,center:0,certain:0,chang:0,channel:0,charact:0,check:[0,1],check_for_curv_stats_fil:0,check_for_custom_measure_stats_fil:0,check_for_hemi_dependent_fil:0,check_for_hemi_independent_fil:0,check_for_nan:0,check_for_parcellation_stats_fil:0,check_for_segmentation_stats_fil:0,chose:[0,3],chosen:0,click:0,close:0,closest:0,closest_voxels_ras_coord:0,cmap:0,code:0,collect:0,collect_data:0,collect_meta_data:0,color:[0,1,3],color_alpha:0,color_blu:0,color_green:0,color_list:0,color_r:0,color_rgbt_to_rgba:0,colorlut:0,colormap:[0,3],colort:[0,3],colum:0,colum_nam:0,column2_info_dict:0,column:[0,3],column_data:0,column_info_:0,column_nam:0,column_name_for_dict_kei:0,column_name_of_valu:0,com:0,combin:0,combinatin:0,come:[0,1,3],comma:0,command:[0,2,3],comment:0,commisur:0,common:[0,2],commonli:0,compar:0,comparison:0,compat:0,complet:0,compress:0,comput:[0,3],compute_label:0,concatin:0,conf_volume_voxels_cr:0,conform:0,conformed_volume_fil:0,connect:0,consecut:0,consid:0,consider:0,consist:[0,1],construct:0,constructor:0,contain:[0,3],content:2,continu:[0,3],contrari:0,conveni:0,convent:0,convert:0,coolwarm:0,coord:0,coordin:[0,1],coordinatesystem:0,coords_3d:0,coords_a2:0,coords_s2a:0,copi:0,coron:0,correct:0,correspond:0,cortex:0,cortic:0,corticalparcel:0,could:0,count:0,cours:0,covari:0,covert:0,creat:0,csv:0,current:0,curv:[0,3],curv_fil:[0,3],curvatur:[0,3],curvind:0,custom:[0,3],custom_cmap:0,custom_morphometry_fil:0,custom_morphometry_file_templ:0,cutom:0,cvs_avg35_inmni152:0,dat:0,data:[0,1,2],data_norm:0,dataformat:0,datafram:0,datastructur:[0,3],datatyp:0,decod:0,defin:0,definit:0,deg2rad:0,deg:0,degre:0,delim:0,delimit:0,demonstr:1,dens:0,depend:0,depth:0,deriv:0,describ:0,descript:0,descriptor:0,descriptor_nam:0,descriptor_valu:0,descriptors_over_threshold:0,design:0,desikan:[0,2],destin:0,destrieux:[0,2],detail:[0,1],detect_subjects_in_directori:0,determin:0,dev:0,dict:0,dictionari:[0,3],did:0,differ:[0,3],dimens:0,dimension:0,dir:0,direct:0,directli:0,directori:[0,3],discov:0,displai:0,display_subject:0,display_surf:0,dist:0,distanc:0,diverg:0,dkt:[0,3],dktatla:[0,3],dktatlas40:0,do_subject_files_exist:0,doc:0,doc_m2html:0,document:3,doe:0,done:0,dot:0,doubl:0,dtype:0,each:[0,3],easili:0,edg:0,edu:0,eeg:0,element:0,els:0,empti:0,enclos:0,encod:0,end:0,end_index:0,enforc:0,entir:0,entri:0,environ:[0,3],equal:0,equival:0,error:0,especi:0,euclidian:0,even:0,everi:0,everyth:0,exact:0,exactli:[0,3],exampl:[0,1,2],exce:0,except:0,exchang:0,exclus:0,execut:0,exist:[0,3],exp_k:0,expect:0,explain:0,explicit:0,explicitli:3,extens:0,extract:0,extract_column_from_table_data:0,extract_field_from_table_data:0,extract_table_data_indices_wher:0,eye:0,face:[0,1,3],fact:0,factor:0,fake:0,fall:0,fals:0,favorit:0,featur:0,field:0,file:[0,1,3],file_ext:0,file_nam:0,file_path:0,filebasedimag:0,filenam:0,filename_templ:0,filesystem:0,fill:0,fill_template_filenam:0,find:0,fine:0,first:[0,3],first_column_nam:0,fit:0,fix:0,float64:0,float_:0,floor:0,fmrib:0,foldind:0,follow:[0,3],format:[0,1],former:0,formleri:0,found:[0,3],frame:0,freeform:0,freesurf:[0,1,3],freesurfer_dir:3,freesurfer_hom:[0,3],freesurfer_surf2voxel:0,freesurfer_vers:0,freesurfercolorlut:0,freesurferdata:2,freesurfersoftwarelicens:0,freeurfer:0,freeview:[0,1],from:[0,1,3],from_list:0,fsaverag:[0,3],fsaverage_mesh:0,fscoord:0,fsd:0,fsl:0,fslwiki:0,fsversion:0,fswiki:0,full:0,fwhm10:0,fwhm20:3,fwhm:[0,3],fwhmx:0,gands_frontomargin:0,gauscurv:0,gener:[0,1],geometri:0,get:[0,2,3],get_affine_matrix_mni152_to_mni305:0,get_affine_matrix_mni305_to_mni152:0,get_atlas_region_nam:0,get_atlas_region_names_hardcod:0,get_closest_not_unknown:0,get_closest_vertex:0,get_closest_vertex_and_dist:0,get_equivalent_voxel_of_raw_volume_in_conformed_volum:0,get_freesurfer_matrix_ras2vox:0,get_freesurfer_matrix_vox2ra:0,get_morphometry_file_path:0,get_n_neighborhood_indices_3d:0,get_n_neighborhood_indices_3d_point:0,get_n_neighborhood_start_stop_indices_3d:0,get_n_neighborhood_start_stop_indices_3d_point:0,get_neighbors_up_to_dist:0,get_num_fsaverage_verts_per_hemi:0,get_ras_coords_at_voxel_cr:0,get_standard_space_morphometry_file_path:0,get_stats_table_column_nam:0,get_surface_file_path:0,get_surface_vertices_overlay_text_file_lin:0,get_surface_vertices_overlay_volume_data:0,get_surface_vertices_overlay_volume_data_1color:0,get_vertex_label_color:0,get_vertex_label_nam:0,get_volume_data_with_custom_mark:0,get_vox2ras_and_ras2vox_from_nifti_fil:0,get_voxel_crs_at_ras_coord:0,get_voxel_segmentation_label:0,getenv:[0,3],github:0,give:0,given:[0,1],grahamwideman:0,grai:0,graph:0,grayvol:0,green:0,group:[0,2],group_md:[0,3],group_meta_data:0,group_morphometry_data:0,group_n:[0,3],group_stat:0,group_stats_aparc:0,group_stats_aparc_a2009:0,group_stats_aparc_dktatla:0,group_stats_aseg:0,group_stats_by_row:0,guarante:0,guess:0,gyrifiact:0,gzip:0,h_morphometry_data_fil:0,hack:0,handl:0,happen:0,hard:0,hardcod:0,harvard:0,has:[0,2],has_header_lin:0,have:[0,3],head:0,header:0,height:0,heinz:0,help:[0,2],hemi:[0,3],hemi_rang:0,hemispher:[0,3],hemisphere_label:0,hemispjer:0,here:[0,3],high:0,highest:0,hint:0,hold:0,home:[0,3],hop:0,horizont:0,how:[0,3],howev:0,htm:0,html:0,http:0,ident:0,identifi:0,ido:0,ids:0,idx:0,ignor:0,ignore_dir_nam:0,ignored_lin:0,illustr:3,imag:0,implement:0,includ:0,inclus:0,increas:0,independ:0,index:[0,2,3],index_of_subject_id_field:0,indic:[0,3],individu:0,inferior:0,inflat:0,inform:[0,3],inherit:0,initi:0,inner:0,input:0,instal:0,instanc:0,instead:[0,3],int32:0,integ:0,intend:0,intens:0,intenstii:0,interact:0,interest:[0,3],interfac:0,inv:0,invers:0,invert:0,item:0,its:[0,1],itself:0,join:[0,3],just:0,kei:0,killiani:[0,3],know:[0,3],kwarg:0,label:[0,3],label_color:[0,3],label_column_index:0,label_fil:0,label_nam:[0,3],label_to_mask:0,labelsclutsannotationfil:0,larg:0,larger:0,last:[0,3],later:0,latter:0,lead:0,least:0,left:0,lefthemi:0,len:0,length:0,let:[0,3],level:0,lh_morphometry_data:0,lh_morphometry_data_fil:0,lh_morphometry_fil:0,lh_surf_fil:0,librari:1,licens:0,lie:0,lies:0,like:[0,1,3],limit:0,line:[0,2],line_sep:0,linear:0,linearsegmentedcolormap:0,link:0,list:[0,3],load:[0,2],load_morphometry_data:0,load_subject_mesh_fil:0,load_subject_morphometry_data_fil:0,load_surface_fil:0,load_vertex_indic:0,load_voxel_indic:0,local:[0,3],locat:0,log:0,look:[0,3],lookup:0,lookup_fil:0,lying:0,m3z:0,m3z_file:0,made:0,mai:[0,3],make:[0,1],mani:[0,3],manual:0,map:[0,2],mark:0,mask:0,mask_data_using_label:0,match:0,matlab:0,matplotlib:0,matplotlib_cmap_nam:0,matric:0,matrix:[0,3],matrix_lin:0,matter:0,matthew:0,max:0,mean:[0,3],mean_thickness_in_region_6:0,meancurv:0,measur:[0,3],measure_list:0,measure_nam:0,measures_data:0,measures_to_numpi:0,mention:0,merg:0,merge_morphometry_data:0,merged_data:0,mesh:[0,2],mesh_to_obj:0,mesh_to_pli:0,meshexport:2,meta:0,meta_data:[0,3],metadata_by_subject:3,method:0,mgh:[0,1,3],mgh_data:0,mgh_file:0,mgh_file_nam:0,mgh_meta_data:0,mghformat:0,mghheader:0,mghimag:0,mgz:[0,1],middl:0,min:0,minim:0,mirror:0,mirror_3d_coordinates_at_axi:0,mirror_at_axis_coordin:0,miss:0,mni152:0,mni152_volum:0,mni305:0,mni:0,mnispac:0,mnt:0,mode:0,model:0,modifi:0,modul:2,modulo:0,more:[0,3],morph_file_format:0,morph_list:0,morphdata_by_subject:[0,3],morpholog:0,morphometri:[0,1,2],morphometry_data:[0,3],morphometry_data_arrai:0,morphometry_fil:[0,3],morphometry_file_format:0,morphometry_meta_data:0,most:0,mrc:0,mri:[0,1],mri_convert:0,mri_info:0,mris_read_m3z:0,much:0,multi:0,must:0,muyt:0,my_data:0,my_freesurfer_dir:0,my_study_data:0,my_study_x:0,my_subject_dir:0,my_subjects_dir:0,mymeasure44:0,mystudi:[],myuser:0,n_label:0,n_vertic:0,name:[0,3],name_dtyp:0,name_null_valu:0,names_str:0,namespac:0,nan:0,nan_share_per_descriptor:0,nan_share_per_subject:0,nativ:[0,2],natur:0,ndarrai:0,necessari:0,need:0,neg:0,neighbor:0,neighborhood:0,neighborhood_s:0,nest:0,net:0,networkx:0,neuroimag:0,ngz:0,ni_img:0,nib:0,nibabel:0,nifti1head:0,nifti1imag:0,nifti:0,nifti_fil:0,nii:0,nipi:0,nit:0,nitool:2,nmr:0,non:[0,1],none:0,nonstandard:0,nonzero:0,normal:0,normmax:0,normmean:0,normmin:0,normrang:0,normstddev:0,nose:0,notat:0,note:0,noth:0,now:[0,3],ntablecol:0,num_data_point:0,num_data_row:0,num_entries_per_row:0,num_fac:0,num_labeled_vert:0,num_vert:0,num_vertic:0,num_verts_tot:0,number:[0,3],numer:0,numpi:[0,3],numvert:0,nvoxel:0,obj:0,obj_fil:0,object:0,obvious:0,occur:0,often:[0,3],older:0,omit:0,onc:0,one:[0,3],ones:0,onli:[0,3],oper:[0,3],oppos:0,opposit:0,option:[0,3],order:0,org:0,orient:0,orig:0,orig_id:0,orig_imag:0,origin:0,other:0,otherwis:0,out:0,outer:0,output:0,over:0,overlai:[0,1],overwrit:0,overwritten:0,own:0,packag:0,page:[0,2],pair:0,pairwis:0,panda:0,pane:0,parallel:0,paramet:0,parcel:[0,2],pars:0,parse_curve_stat:0,parse_curve_stats_fil:0,parse_registration_matrix:0,parse_talairach_fil:0,part:0,particip:0,participants_fil:0,participants_id:0,particular:0,pass:0,path:[0,3],paulbourk:0,peopl:0,per:0,per_vertex_data:[0,3],perform:0,perpendicular:0,pial:0,pial_lgi:0,picki:0,pipelin:0,plane:0,plasma:0,plu:0,ply:0,point:0,point_i:0,point_mirror_3d_coordin:0,point_x:0,point_z:0,posit:0,possibl:0,posterior:0,pre:[0,1],preced:0,prefix:0,preprocess:0,preserv:0,pretti:0,previous:0,print:[0,3],problemat:0,proceed:0,process:[0,1],programm:1,proper:0,properti:0,put:0,python:[0,3],qcach:3,qform:0,qualit:0,queri:[0,1],query_coord:0,query_crs_coord:0,query_vertex_indic:0,query_vox_cr:0,query_voxels_cr:0,question:0,quot:0,rad2deg:0,rad:0,radian:0,radians_i:0,radians_x:0,radians_z:0,rais:0,rang:0,ras2vox:0,raw:0,raw_volume_fil:0,raw_volume_query_voxels_cr:0,rawavg:0,read:[0,1],read_annot:0,read_annotation_md:0,read_bids_participants_fil:0,read_fs_morphometry_data_file_and_record_meta_data:0,read_fs_surface_file_and_record_meta_data:0,read_geometri:0,read_label_md:0,read_lookup_fil:0,read_m3z_fil:0,read_mgh_fil:0,read_mgh_header_matric:0,read_subjects_fil:0,read_vertex_list_fil:0,reader:0,readi:0,reason:0,receiv:0,recommend:0,recon:[0,3],record:0,red:0,refer:0,reflect:0,reg_data_fil:0,region:[0,3],region_6_nam:0,region_data:0,region_data_n:0,region_data_per_hemi:0,region_stat:0,regist:0,register_dat_matrix:0,registerdat:0,registr:0,rel:0,relat:0,releas:0,relev:0,reli:[0,3],replac:[0,3],report:0,report_descriptor:0,repositori:0,repres:0,request:[0,1],requested_measur:0,requir:0,required_subdirs_for_hit:0,reset:0,resort:0,respect:0,rest:0,result:0,retriev:0,revers:0,rgb:[0,3],rgba:0,rgbt:0,rh_morphometry_data:0,rh_morphometry_data_fil:0,rh_morphometry_fil:0,rh_relative_index:0,rh_surf_fil:0,rhi:0,rhv:0,right:[0,3],righthemi:0,rotat:0,rotate_3d_coordinates_around_ax:0,roughli:0,row:0,row_index:0,row_indic:0,run:[0,1],run_md:[0,3],run_meta_data:0,s_frontomargin:0,sagit:0,same:[0,3],sapc:0,save:[0,3],save_vertex_indic:0,scalar:0,scalars_to_colors_clist:0,scalars_to_colors_matplotlib:0,scale:0,scale_3d_coordin:0,scan:1,scanner:0,scipi:0,script:0,sdata201644:0,search:[0,2],search_dir:0,searched_fil:0,second:0,section:0,see:[0,3],seem:0,seg_cod:0,seg_nam:0,segid:0,segment:0,segmentation_list:0,select:0,selected_vert_indic:0,sens:0,sep:0,separ:0,sequenti:0,set:0,sever:0,sform:0,shape:0,share:0,shift:0,shift_i:0,shift_x:0,shift_z:0,shortest:0,shoud:3,should:0,show:0,shown:0,similar:0,simpl:0,simpli:0,sinc:0,singl:[0,2],size:0,skip:0,slice:0,smaller:0,smallest:0,smoot:0,smooth:0,softwar:0,solut:0,some:[0,1],some_kei:0,someth:0,sometim:0,someus:0,sourc:0,source_vert:0,sourceforg:0,space:[0,2],spatial:2,special:0,specif:0,specifi:[0,3],spectral:0,sphere:0,split:0,spot:0,squar:0,stack:0,standard:[0,2],start:0,start_index:0,stat:2,statist:0,stats_fil:0,stats_file_nam:0,stats_table_region_label_column_nam:0,stats_table_to_numpi:0,stats_table_to_numpy_by_row:0,stats_table_type_list:0,stdout:0,still:0,stop:0,store:[0,3],str:0,string:0,structnam:0,structur:[0,1],structure_nam:0,studi:[0,1],study1:3,study1_data:0,study5:0,sub:0,sub_dir:0,subdir:0,subj_:0,subjct:0,subject1:[0,3],subject2:0,subject33:0,subject3:0,subject4:[0,3],subject4_idx:[0,3],subject5:3,subject7:0,subject8:0,subject:[0,1,2],subject_avg:[0,3],subject_data_n:0,subject_data_standard:0,subject_dir:0,subject_id:0,subject_mesh:0,subject_surf_dir:0,subjects_detection_mod:0,subjects_detection_mode_auto_used_method:0,subjects_dir:[0,3],subjects_dir_for_average_subject:0,subjects_fil:0,subjects_file_dir:0,subjects_id:0,subjects_list:[0,3],subjects_over_threshold:0,submodul:2,subset:0,substitut:0,substitution_dict:0,subtyp:0,suitabl:0,sum:3,superior:0,suppli:0,support:0,sure:0,surf:[0,1,3],surf_fil:0,surf_raw:0,surfac:[0,1,3],surfacegraph:2,surfarea:0,surfer:0,surpris:0,system:0,t152:0,t305:0,tab10:0,tab20:0,tab:0,tabl:0,table_column_head:0,table_data:0,table_meta_data:0,take:0,taken:0,talairach:0,target:0,target_value_str:0,target_voxel_indic:0,target_voxel_valu:0,task:[0,3],templat:0,template_str:0,test_data_dir:0,text:[0,1],than:0,thei:0,them:[0,1],theoret:0,thi:[0,3],thick:[0,1],thickavg:0,thickstd:0,thin:0,think:0,third:0,those:0,though:0,three:0,threshold:0,thu:0,time:0,ting:0,tissu:0,tkr:0,tkregist:0,to_filenam:0,token:0,too:0,tool:[0,2],top:0,total:0,tranform:0,transform:0,translat:0,translate_3d_coordinates_along_ax:0,transpar:0,transposit:0,travers:0,tri:0,triplet:0,tsv:0,tupel:0,tupl:0,turn:0,two:[0,3],txt:0,type:0,type_list:0,typelist_for_:0,typelist_for_aparc_atlas_stat:0,typelist_for_aseg_stat:0,typic:0,u50:0,ugli:0,uint8:0,unaffect:0,unalt:0,under:0,understand:0,uniqu:[0,3],unitless:0,unix:0,unknown:0,unknown_label:0,unless:0,unsmooth:0,unter:0,until:0,usag:[0,1],use:[0,3],use_freesurfer_home_if_miss:0,use_sform:0,used:[0,3],useful:0,user:0,user_hom:0,uses:0,using:[0,3],usr:3,usual:0,usus:0,utf:0,util:0,v152:0,v305:0,valid:0,valu:[0,1,3],valueerror:0,var_nam:0,variab:0,variabl:[0,3],variou:0,vector:0,ventricl:0,veri:0,verifi:0,version:0,vert:0,vert_coord:[0,3],vert_idx:0,vertcount:0,vertex:[0,1,3],vertex_color:0,vertex_coord:0,vertex_indic:0,vertex_indices_fil:0,vertex_label:[0,3],vertex_label_color:0,vertex_lookup_indic:0,vertex_mark_list:0,vertic:[0,1,3],vertices_to_label:0,verts_in_label:0,view:0,viewer:0,viridi:0,visual:[0,1],visualize_vert:1,vloc:0,vol_data:0,vol_dest:0,vol_ind0:0,vol_orig:0,volum:[0,1],volume_fil:0,volume_mm3:0,volume_shap:0,vox2ra:0,vox2ras_tkr:0,vox:0,voxel:[0,1],voxel_data:0,voxel_mark_list:0,voxel_seg_cod:0,voxel_seg_nam:0,wai:[0,3],want:[0,3],warn:0,wavefront:0,wavefront_:0,weird:0,well:0,were:[0,3],what:[0,3],whatev:0,when:[0,3],where:0,wherev:3,whether:[0,1],which:[0,1,3],white:[0,1,3],whole:0,width:0,wiki:0,wikipedia:0,wise:0,within:0,word:0,word_her:0,work:[0,3],workflow:2,world:0,worri:0,would:0,wrapper:0,write:0,write_bids_participants_fil:0,write_lines_to_text_fil:0,write_subjects_fil:0,write_voldata_to_mgh_fil:0,write_voldata_to_nifti_fil:0,written:0,www:0,x_mirror:0,x_scale:0,x_scale_factor:0,x_shift:0,xend:0,xfm:0,xstart:0,xyz:0,y_mirror:0,y_scale:0,y_scale_factor:0,y_shift:0,yend:0,yet:0,you:[0,3],your:[0,3],yourself:0,ystart:0,z_mirror:0,z_scale:0,z_scale_factor:0,z_shift:0,zend:0,zero:0,zstart:0},titles:["Brainload API Documentation","Brainload Command Line Tools","Welcome to brainload\u2019s documentation!","Brainload Example Workflows"],titleterms:{annot:0,api:0,atla:3,avail:1,been:3,brain:3,braindescriptor:0,brainload:[0,1,2,3],brainloc:0,brainvoxloc:0,brainwrit:0,command:1,common:3,data:3,desikan:3,destrieux:3,document:[0,2],exampl:3,freesurferdata:0,get:1,group:3,has:3,help:1,indic:2,line:1,load:3,map:3,mesh:3,meshexport:0,modul:0,morphometri:3,nativ:3,nitool:0,parcel:3,singl:3,space:3,spatial:0,standard:3,stat:0,subject:3,submodul:0,surfacegraph:0,tabl:2,tool:1,welcom:2,workflow:3}})