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AFNI_CoordChange.m File Reference

Go to the source code of this file.


Functions

like RAI or[1 3 4] Mtrans
is Morig in the new coordinate
system Key 		Mtrans (:, i)
 if (nargin==2)
end if (~isempty(Morig)&size(Morig, 2)~=3)
 if (ischar(Orig))
end if (ischar(Trans))
end for (i=1:1:3)
 if (~isempty(itmp))
no need for flipping maplocation (i)
 mapsign (i)
else look for opposite need
flipping 		if (rem(TrCode(i), 2))
 if (isempty(itmp))
end end for i if (~isempty(Morig))

Variables

 function [err, maplocation, mapsign, Mtrans]
like RAI or[1 3 4] Trans
like RAI or[1 3 4] Mtrans
is Morig in the new coordinate
system Key 		Terms
end example
end maplocation = [0 0 0]
end mapsign = [0 0 0]
end Mtrans
end Bethesda Maryland Define
the function name for easy
referencing 		FuncName = 'AFNI_CoordChange'
Debug Flag DBG = 1
 Morig = []
end err = ErrEval(FuncName,'Err_Bad size for Morig')
 return
else OrCode = AFNI_OrientCode (Orig) Orig
end else TrCode = AFNI_OrientCode (Trans) Trans
end look for the orientation itmp = find (OrCode == TrCode(i))
 found = j
else look for opposite orientation
else look for opposite need
flipping 		shft = -1

Function Documentation

end for (  i  = 1:1:3  ) 
 

end end for i if (  ~  isempty(Morig)  ) 
 

if (  isempty(itmp)   ) 
 

else look for opposite need flipping if (  rem(TrCode(i), 2)   ) 
 

if (  ~  isempty(itmp)  ) 
 

end if (  ischar(Trans)   ) 
 

if (  ischar(Orig)   ) 
 

end if (  ~isempty(Morig)&size(Morig, 2)~  = 3  ) 
 

if (  nargin  = = 2  ) 
 

Referenced by Gif_XSubImageColormap(), globfree(), GRA_drawing_EV(), put_sub_image_colormap(), SUMA_AddDsetColAttr(), SUMA_AddGenDsetColAttr(), SUMA_ClusterCenterofMass(), SUMA_FaceSet_Edge_Neighb(), SUMA_Find_IminImax(), SUMA_FindEdgeInTri(), SUMA_Free_CommSrtuct(), SUMA_free_FaceSet_Edge_Neighb(), SUMA_FreeGenericArgParse(), SUMA_Get_Incident(), SUMA_Get_NodeIncident(), SUMA_GetDsetColRange(), SUMA_GetM2M_NN(), SUMA_GetOverlaysFromParent(), SUMA_LinkTailNodeToNodeStroke(), SUMA_LinkThisNodeToNodeInStroke(), SUMA_NodeStrokeToConnectedNodes(), SUMA_Parse_IO_Args(), SUMA_Read_Color_Map_1D(), SUMA_RegisterEngineListCommand(), SUMA_SkullMask(), SUMA_Sort_ClustersList(), SUMA_SwitchSO(), and volume_search().

no need for flipping maplocation (  i   ) 
 

mapsign (  i   ) 
 

like RAI or [1 3 4] Mtrans is Morig in the new coordinate system Key Mtrans (  :  ,
i 
) 
 

Variable Documentation

Debug Flag DBG = 1
 

Definition at line 47 of file AFNI_CoordChange.m.

end err = ErrEval(FuncName,'Err_Bad size for Morig')
 

Definition at line 104 of file zglobb.m.

end example
 

Definition at line 36 of file AFNI_CoordChange.m.

else found = j
 

Definition at line 155 of file Read_1D.m.

Referenced by colormap_combine(), convert1(), DCM_GetElementValueList(), DCM_GetSequenceElement(), DCM_GetSequenceList(), DCM_LookupElement(), DCM_RemoveGroup(), DCM_ScanParseObject(), e_d(), find_fl_file_index(), hash_color(), iocname(), locateElement(), read_text_colormap(), segment_x_slices(), segment_y_slices(), segment_z_slices(), SUMA_Addto_ROIplane_List(), SUMA_binSearch(), SUMA_cb_search_text(), SUMA_inNodeNeighb(), SUMA_M2M_node_Info(), SUMA_MapSurface(), SUMA_OpenDrawnROI_NIML(), SUMA_ShowAllVisuals(), and try_assign_transparency().

end setup the new header and write out the files FuncName = 'AFNI_CoordChange'
 

Definition at line 151 of file ResliceBrick.m.

Referenced by calcWithOffsets(), cmp_surf_usage(), main(), SUMA_1DROI_to_DrawnROI(), SUMA_2Prefix2SurfaceName(), SUMA_3dBRAIN_VOYAGERtoAFNI_ParseInput(), SUMA_3dCRUISEtoAFNI_ParseInput(), SUMA_3dSurfMask_ParseInput(), SUMA_Add_Color(), SUMA_Add_ColorMap(), SUMA_AddColAtt_CompString(), SUMA_AddColAttr(), SUMA_AddDO(), SUMA_AddDsetColAttr(), SUMA_AddFillROIDatum(), SUMA_AddLink(), SUMA_AddNelHist(), SUMA_AddNewPlane(), SUMA_AddNgrHist(), SUMA_addNode(), SUMA_AddNodeIndexColumn(), SUMA_AddNodeToLayer(), SUMA_Addto_ROIplane_List(), SUMA_AddToBrushStroke(), SUMA_AddToTailJunctionROIDatum(), SUMA_AddToTailROIDatum(), SUMA_addTri(), SUMA_AdoptGroup(), SUMA_AdoptSurfGroup(), SUMA_AdvancePastNumbers(), SUMA_AFNI_Extract_Colors(), SUMA_AFNI_forward_warp_xyz(), SUMA_AfniExists(), SUMA_AfniExistsView(), SUMA_AfniPrefix(), SUMA_AFNItlrc_toMNI(), SUMA_AfniView(), SUMA_Align_to_VolPar(), SUMA_All_Programs(), SUMA_Alloc_Axis(), SUMA_Alloc_CrossHair(), SUMA_Alloc_DisplayObject_Struct(), SUMA_Alloc_FaceSetMarker(), SUMA_Alloc_OpenDX_Struct(), SUMA_alloc_problem(), SUMA_Alloc_SegmentDO(), SUMA_Alloc_SphereMarker(), SUMA_Alloc_SurfaceViewer_Struct(), SUMA_Alloc_SurfObject_Struct(), SUMA_Alloc_ViewState(), SUMA_Alloc_ViewState_Hist(), SUMA_Alloc_VolPar(), SUMA_allocate2D(), SUMA_Allocate_SPI(), SUMA_AllocateDrawnROI(), SUMA_AllocateROI(), SUMA_AllocateScrolledList(), SUMA_AllocROIDatum(), SUMA_AllocTableField(), SUMA_append_replace_string(), SUMA_append_string(), SUMA_AppendToROIdatum(), SUMA_Apply_VolReg_Trans(), SUMA_ApplyAffine(), SUMA_AreaDiff(), SUMA_AskUser_File_replace(), SUMA_AssembleAllROIList(), SUMA_AssembleCmapList(), SUMA_AssembleColorPlaneList(), SUMA_AssembleGroupList(), SUMA_assignColors(), SUMA_AssignTriBranch(), SUMA_ATF_cb_label_change(), SUMA_ATF_cb_label_Modify(), SUMA_ATF_change_value(), SUMA_ATF_SetString(), SUMA_ATF_SetValue(), SUMA_ATF_start_stop(), SUMA_AttrOfDsetColNumb(), SUMA_AxisText(), SUMA_BestStandardView(), SUMA_BinarySuck(), SUMA_BinaryZeroSearch(), SUMA_binSearch(), SUMA_binTesselate(), SUMA_BrainVoyager_Read(), SUMA_BrainVoyager_Read_vmr(), SUMA_BreakInodeLink(), SUMA_BrushStrokeToNodeStroke(), SUMA_Build_Cluster_From_Node(), SUMA_Build_Cluster_From_Node_NoRec(), SUMA_Build_Color_maps(), SUMA_Build_FirstNeighb(), SUMA_Build_Mask_AllROI(), SUMA_Build_Mask_DrawnROI(), SUMA_build_rotmatrix(), SUMA_BuildMenu(), SUMA_BuildMenuReset(), SUMA_BuildMessageLog(), SUMA_ButtClose_pushed(), SUMA_ButtOpen_pushed(), SUMA_CalcNeighbDist(), SUMA_CalculateNodeAreas(), SUMA_CanTalkToAfni(), SUMA_Cart2Sph(), SUMA_cb_AbsThresh_tb_toggled(), SUMA_cb_AfniLink_toggled(), SUMA_cb_CloseDrawROIWindow(), SUMA_cb_closeSumaCont(), SUMA_cb_closeSurfaceCont(), SUMA_cb_CloseSwitchCmap(), SUMA_cb_CloseSwitchColPlane(), SUMA_cb_CloseSwitchGroup(), SUMA_cb_CloseSwitchROI(), SUMA_cb_closeViewerCont(), SUMA_cb_Cmap_Load(), SUMA_cb_ColPlane_Delete(), SUMA_cb_ColPlane_Load(), SUMA_cb_ColPlaneShow_toggled(), SUMA_cb_ColPlaneShowOne_toggled(), SUMA_cb_createSumaCont(), SUMA_cb_createSurfaceCont(), SUMA_cb_createViewerCont(), SUMA_cb_doneSumaCont(), SUMA_cb_DrawROI_Delete(), SUMA_cb_DrawROI_Finish(), SUMA_cb_DrawROI_Join(), SUMA_cb_DrawROI_Load(), SUMA_cb_DrawROI_Redo(), SUMA_cb_DrawROI_Save(), SUMA_cb_DrawROI_SwitchROI(), SUMA_cb_DrawROI_Undo(), SUMA_cb_DrawROImode_toggled(), SUMA_cb_DrawROIPen_toggled(), SUMA_cb_Dset_Load(), SUMA_cb_FileClose(), SUMA_cb_FileLoadView(), SUMA_cb_FileOpenSpec(), SUMA_cb_FileOpenSurf(), SUMA_cb_FileSaveView(), SUMA_cb_helpIO_notify(), SUMA_cb_helpMemTrace(), SUMA_cb_helpMessageLog(), SUMA_cb_helpSUMAGlobal(), SUMA_cb_helpSurfaceStruct(), SUMA_cb_helpUsage(), SUMA_cb_helpViewerStruct(), SUMA_cb_moreSumaInfo(), SUMA_cb_moreSurfInfo(), SUMA_cb_moreViewerInfo(), SUMA_cb_newSumaCont(), SUMA_cb_search_text(), SUMA_cb_SelectSwitchCmap(), SUMA_cb_SelectSwitchColPlane(), SUMA_cb_SelectSwitchGroup(), SUMA_cb_SelectSwitchROI(), SUMA_cb_set_threshold(), SUMA_cb_set_threshold_label(), SUMA_cb_SetCmapMode(), SUMA_cb_SetCoordBias(), SUMA_cb_SetDrawROI_SaveMode(), SUMA_cb_SetDrawROI_SaveWhat(), SUMA_cb_SetDrawROI_WhatDist(), SUMA_cb_SetRenderMode(), SUMA_cb_ShowZero_tb_toggled(), SUMA_cb_SurfCont_SwitchColPlane(), SUMA_cb_SwitchBrightness(), SUMA_cb_SwitchCmap(), SUMA_cb_SwitchIntensity(), SUMA_cb_SwitchThreshold(), SUMA_cb_SwithBrt_toggled(), SUMA_cb_SwithInt_toggled(), SUMA_cb_SwithThr_toggled(), SUMA_cb_SymIrange_tb_toggled(), SUMA_cb_toggle_crosshair(), SUMA_cb_toggle_node_in_focus(), SUMA_cb_toggle_selected_faceset(), SUMA_cb_ToggleCaseSearch(), SUMA_cb_ToolsDrawROI(), SUMA_cb_UnmanageWidget(), SUMA_cb_ViewerCont_SwitchGroup(), SUMA_cb_ViewerCont_SwitchState(), SUMA_cb_viewSumaCont(), SUMA_cb_viewSurfaceCont(), SUMA_cb_viewViewerCont(), SUMA_cb_XHalock_toggled(), SUMA_cb_XHaviewlock_toggled(), SUMA_cb_XHlock_toggled(), SUMA_cb_XHviewlock_toggled(), SUMA_cellvariety(), SUMA_CheckOnSpecFile(), SUMA_Chung_Smooth(), SUMA_Chung_Smooth_Weights(), SUMA_ClassOf(), SUMA_ClearBrushStroke(), SUMA_ClusterCenterofMass(), SUMA_cmap_context_Init(), SUMA_Cmap_To_SO(), SUMA_Cmap_To_SO_old(), SUMA_cmap_wid_display(), SUMA_cmap_wid_expose(), SUMA_cmap_wid_graphicsInit(), SUMA_cmap_wid_handleRedisplay(), SUMA_cmap_wid_input(), SUMA_cmap_wid_postRedisplay(), SUMA_cmap_wid_resize(), SUMA_CmapOfPlane(), SUMA_CmapSelectList(), SUMA_coarsen_ParseInput(), SUMA_Col2Float(), SUMA_Col_Type(), SUMA_Col_Type_Name(), SUMA_ColLabelCopy(), SUMA_ColMixModeString(), SUMA_ColorizePlane(), SUMA_ColorMapVec_Info(), SUMA_ColorOverlayPlane_Info(), SUMA_ColorVec_Info(), SUMA_ColPlane_NewDimFact(), SUMA_ColPlane_NewOpacity(), SUMA_ColPlane_NewOrder(), SUMA_ColType2TypeCast(), SUMA_CommandCode(), SUMA_CommandString(), SUMA_CommonFieldsInfo(), SUMA_comp_str_2_NI_str_ar(), SUMA_context_Init(), SUMA_ConvexHullSurface(), SUMA_Convexity(), SUMA_Convexity_Engine(), SUMA_CoordChange(), SUMA_Copy_Part_Column(), SUMA_copy_string(), SUMA_Create_1dData(), SUMA_Create_ColorScaledVect(), SUMA_Create_CommonFields(), SUMA_Create_CommSrtuct(), SUMA_Create_IRGB(), SUMA_Create_MemTrace(), SUMA_Create_MorphInfo(), SUMA_Create_SO_map(), SUMA_CreateActionStack(), SUMA_CreateArrowField(), SUMA_CreateAssembleListStruct(), SUMA_CreateBrushStroke(), SUMA_CreateBSDatum(), SUMA_CreateChildSO(), SUMA_CreateCmapWidgets(), SUMA_createColGradient(), SUMA_CreateDrawROIStruct(), SUMA_CreateDrawROIWindow(), SUMA_CreateDsetPointer(), SUMA_CreateFileSelectionDialog(), SUMA_CreateFileSelectionDialogStruct(), SUMA_CreateFS_ColorTable(), SUMA_CreateIcosahedron(), SUMA_CreateInode(), SUMA_CreateInodeLink(), SUMA_CreateList(), SUMA_CreateLock_rbg(), SUMA_CreateMessageList(), SUMA_CreateOverlayPointer(), SUMA_CreatePromptActionArea(), SUMA_CreatePromptDialog(), SUMA_CreatePromptDialogStruct(), SUMA_CreateScrolledList(), SUMA_CreateSumaContStruct(), SUMA_CreateSurfContStruct(), SUMA_CreateTable(), SUMA_CreateTextField(), SUMA_CreateTextShell(), SUMA_CreateTextShellStruct(), SUMA_CreateUpdatableCmapMenu(), SUMA_CreateViewContStruct(), SUMA_CreateXhairWidgets(), SUMA_delete_timeout_CB(), SUMA_DeleteROI(), SUMA_DestroyAfniColors(), SUMA_DestroyList(), SUMA_DestroyROIActionData(), SUMA_DestroyTextShell(), SUMA_detWeight(), SUMA_Dijkstra(), SUMA_disp_dmat(), SUMA_disp_dvect(), SUMA_disp_mat(), SUMA_disp_vecdmat(), SUMA_disp_vecmat(), SUMA_disp_vect(), SUMA_disp_vecucmat(), SUMA_display(), SUMA_divEdge(), SUMA_DomainKinships_String(), SUMA_dPercRange(), SUMA_dPoint_At_Distance(), SUMA_dqsortrow(), SUMA_Draw_SO_ROI(), SUMA_DrawAxis(), SUMA_DrawBrushStroke(), SUMA_DrawCmap(), SUMA_DrawCrossHair(), SUMA_DrawFaceSetMarker(), SUMA_DrawLineAxis(), SUMA_DrawMesh(), SUMA_DrawnROI_to_1DDrawROI(), SUMA_DrawnROI_to_NIMLDrawnROI(), SUMA_DrawROI_NewLabel(), SUMA_DrawROI_NewValue(), SUMA_DrawSegmentDO(), SUMA_DrawWindowLine(), SUMA_Dset_Format(), SUMA_Dset_Format_Name(), SUMA_Dset_Type(), SUMA_Dset_Type_Name(), SUMA_DsetCol2Float(), SUMA_DsetColLabelCopy(), SUMA_DsetColSelectList(), SUMA_DsetInfo(), SUMA_EmptyColorList(), SUMA_EmptyDestroyActionStack(), SUMA_EmptyDestroyList(), SUMA_Engine(), SUMA_EngineFieldCode(), SUMA_EngineFieldString(), SUMA_EngineSourceCode(), SUMA_EngineSourceString(), SUMA_EquateSurfaceAreas(), SUMA_EquateSurfaceSize(), SUMA_EquateSurfaceVolumes(), SUMA_error_message(), SUMA_etime(), SUMA_existDO(), SUMA_existSO(), SUMA_expose(), SUMA_Extension(), SUMA_EyeAxisStandard(), SUMA_far2dset(), SUMA_Fetch_OverlayPointer(), SUMA_FetchROI_InCreation(), SUMA_file_suck(), SUMA_FileSelection_file_select_cb(), SUMA_FileSelection_popdown_cb(), SUMA_FileSelection_Unmap_cb(), SUMA_filexists(), SUMA_FillColorList(), SUMA_FillDsetNelCol(), SUMA_FillNelCol(), SUMA_FillToMask(), SUMA_FillToMask_Engine(), SUMA_FillToVoxelMask(), SUMA_Find_Edge_Nhost(), SUMA_Find_IminImax(), SUMA_Find_inIntVect(), SUMA_find_named_SOp_inDOv(), SUMA_Find_OpenDX_Object_Class(), SUMA_Find_OpenDX_Object_Name(), SUMA_Find_ROIonSO(), SUMA_Find_ROIrelatedtoSO(), SUMA_FindClusters(), SUMA_FindDset(), SUMA_FindDsetAttributeElement(), SUMA_FindDsetDataAttributeElement(), SUMA_FindNgrAttributeElement(), SUMA_findSO_inDOv(), SUMA_findSOp_inDOv(), SUMA_FindVoxelsInSurface(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_FinishedROI(), SUMA_Flip_Color_Map(), SUMA_flip_orient(), SUMA_float_file_size(), SUMA_FlushPlaneNotInUse(), SUMA_ForceUser_YesNo(), SUMA_FormAfnidset(), SUMA_Format(), SUMA_FormatMessage(), SUMA_FormNeighbOffset(), SUMA_FormSOListToSendToAFNI(), SUMA_FormSwitchCmapMenuVector(), SUMA_FormSwitchColMenuVector(), SUMA_fqsortrow(), SUMA_free2D(), SUMA_Free_1dData(), SUMA_Free_1DDrawROI(), SUMA_Free_Axis(), SUMA_Free_ColorMap(), SUMA_Free_ColorScaledVect(), SUMA_Free_CommonFields(), SUMA_Free_CrossHair(), SUMA_Free_Displayable_Object(), SUMA_Free_Displayable_Object_Vect(), SUMA_free_Edge_List(), SUMA_Free_FaceSetMarker(), SUMA_Free_FirstNeighb(), SUMA_Free_FormAfniDset_Opt(), SUMA_Free_FreeSurfer(), SUMA_Free_getoffsets(), SUMA_Free_IRGB(), SUMA_Free_IsInBox(), SUMA_Free_IsInSphere(), SUMA_Free_MemberFaceSets(), SUMA_Free_MemTrace(), SUMA_Free_MorphInfo(), SUMA_Free_MT_intersect_triangle(), SUMA_free_NeighbOffset(), SUMA_free_NI_str_array(), SUMA_Free_NIMLDrawROI(), SUMA_Free_OpenDX_Struct(), SUMA_Free_OpenDX_StructVec(), SUMA_Free_Parsed_Name(), SUMA_Free_ROI_PlaneData(), SUMA_free_SegmentDO(), SUMA_Free_SO_map(), SUMA_Free_SphereMarker(), SUMA_free_SPI(), SUMA_free_STB(), SUMA_Free_SureFit(), SUMA_Free_SURFACE_CURVATURE(), SUMA_Free_Surface_Object(), SUMA_Free_SurfaceViewer_Struct(), SUMA_Free_SurfaceViewer_Struct_Vect(), SUMA_Free_ViewState(), SUMA_Free_ViewState_Hist(), SUMA_Free_VolPar(), SUMA_FreeActionStackData(), SUMA_FreeAssembleListStruct(), SUMA_FreeBSDatum(), SUMA_FreeClustDatum(), SUMA_freeDrawnROI(), SUMA_FreeDrawROIStruct(), SUMA_FreeDset(), SUMA_FreeEngineData(), SUMA_FreeEngineListData(), SUMA_FreeFileSelectionDialogStruct(), SUMA_FreeFS_ColorTable(), SUMA_FreeLock_rbg(), SUMA_FreeM2M(), SUMA_FreeMenuVector(), SUMA_FreeMessageListData(), SUMA_FreeNewSOOpt(), SUMA_FreeOverlayListDatum(), SUMA_FreeOverlayPointer(), SUMA_freePatch(), SUMA_FreePromptDialogStruct(), SUMA_freeROI(), SUMA_FreeROIDatum(), SUMA_FreeScrolledList(), SUMA_FreeSumaContStruct(), SUMA_FreeSurfContStruct(), SUMA_FreeSurfer_Read(), SUMA_FreeSurfer_Read_eng(), SUMA_FreeSurfer_ReadBin_eng(), SUMA_FreeSurfer_WritePatch(), SUMA_FreeTableField(), SUMA_FreeViewContStruct(), SUMA_FromIntEdgeToIntEdge(), SUMA_FromToRotation(), SUMA_FS_ColorTable_Info(), SUMA_FS_Write(), SUMA_generateEPS(), SUMA_Get_AFNI_Default_Color_Maps(), SUMA_get_fallbackResources(), SUMA_Get_isosurface_datasets(), SUMA_Get_Sub_String(), SUMA_GetAreaDiffRange(), SUMA_GetColIndex(), SUMA_GetColorList(), SUMA_GetContour(), SUMA_GetCx(), SUMA_GetDO_Type(), SUMA_GetDsetColIndex(), SUMA_GetDsetValInCol(), SUMA_GetDsetValInCol2(), SUMA_GetEyeAxis(), SUMA_GetLargestBackroundOrder(), SUMA_GetListNextCommand(), SUMA_GetM2M_NN(), SUMA_GetNextCommand(), SUMA_GetNgrHist(), SUMA_GetNodeDef(), SUMA_GetNodeIndex_FromNodeRow(), SUMA_GetNodeOverInd(), SUMA_GetNodeRow_FromNodeIndex(), SUMA_GetOffset2Offset(), SUMA_getoffsets(), SUMA_getoffsets2(), SUMA_getoffsets_ll(), SUMA_getPatch(), SUMA_GetSelectionLine(), SUMA_getShareableColormap(), SUMA_getShareableColormap_Eng(), SUMA_GetSmallestForegroundOrder(), SUMA_GetStandardMap(), SUMA_GetValInCol(), SUMA_GetValInCol2(), SUMA_GetVolDiffRange(), SUMA_GimmeSomeSOs(), SUMA_grabPixels(), SUMA_graphicsInit(), SUMA_guess_surftype_argv(), SUMA_GuessAnatCorrect(), SUMA_GuessFormatFromExtension(), SUMA_GuessSide(), SUMA_handleRedisplay(), SUMA_Help_AllSurfCont(), SUMA_help_basics(), SUMA_Help_Cmap_destroyed(), SUMA_help_Cmap_message_Info(), SUMA_Help_Cmap_open(), SUMA_Help_destroyed(), SUMA_help_message(), SUMA_help_message_Info(), SUMA_Help_open(), SUMA_help_talk(), SUMA_HighlightBox(), SUMA_HistString(), SUMA_Householder(), SUMA_Init_SurfCont_CrossHair(), SUMA_Init_SurfCont_SurfParam(), SUMA_Initialize_getoffsets(), SUMA_InitializeColPlaneShell(), SUMA_InitializeDrawROIWindow(), SUMA_InitializeEngineListData(), SUMA_InitRangeTable(), SUMA_inNodeNeighb(), SUMA_input(), SUMA_InsertDsetPointer(), SUMA_Interpret_AFNIColor(), SUMA_IntersectionStrip(), SUMA_IO_args_2_spec(), SUMA_iRGB_to_OverlayPointer(), SUMA_is_AllNumeric_dset(), SUMA_is_AllNumeric_nel(), SUMA_is_AllNumeric_ngr(), SUMA_isConsistent(), SUMA_isdROIrelated(), SUMA_isDsetColumn_inferred(), SUMA_isDsetRelated(), SUMA_isExtension(), SUMA_isinbox(), SUMA_isINHmappable(), SUMA_isInodeLink(), SUMA_isinpoly(), SUMA_isinsphere(), SUMA_isLocalDomainParent(), SUMA_ismappable(), SUMA_isNumString(), SUMA_isOverlayOfSO(), SUMA_isRelated(), SUMA_isROIdequal(), SUMA_isROIrelated(), SUMA_isSameEdge(), SUMA_isSelfIntersect(), SUMA_isSkin(), SUMA_isSO(), SUMA_isSO_G(), SUMA_isTriLinked(), SUMA_isTypicalSOforVolSurf(), SUMA_isVisibleSO(), SUMA_iswordin(), SUMA_iswordin_ci(), SUMA_IV_FaceSetsextract(), SUMA_IV_XYZextract(), SUMA_JumpFocusFace(), SUMA_JumpFocusNode(), SUMA_JumpIndex(), SUMA_JumpXYZ(), SUMA_leave_EV(), SUMA_leave_TableField(), SUMA_Linearize_Color_Map(), SUMA_LinkToPointer(), SUMA_ListOrderToPlaneOrder(), SUMA_Load1DDset(), SUMA_Load_Spec_Surf(), SUMA_Load_Surface_Object(), SUMA_Load_Surface_Object_eng(), SUMA_Load_Surface_Object_Wrapper(), SUMA_LoadCmapFile(), SUMA_LoadColorPlaneFile(), SUMA_LoadDset(), SUMA_LoadDsetFile(), SUMA_LoadDXDset(), SUMA_LoadNimlDset(), SUMA_LoadPrepInVol(), SUMA_LoadSegDO(), SUMA_LoadSpec(), SUMA_LoadSpec_eng(), SUMA_LoadVisualState(), SUMA_LockEnum_LockType(), SUMA_LookAtCoordinates(), SUMA_M2M_interpolate(), SUMA_M2M_node_Info(), SUMA_Make_Edge_List(), SUMA_Make_Edge_List_eng(), SUMA_MakeColorMap(), SUMA_MakeColorMap_v2(), SUMA_MakeConsistent(), SUMA_makeNI_CrossHair(), SUMA_makeNI_SurfIJK(), SUMA_makeNI_SurfINORM(), SUMA_makeNI_SurfIXYZ(), SUMA_MapRefRelative(), SUMA_mapStateChanged(), SUMA_MapSurface(), SUMA_MarchingCubesSurface(), SUMA_Mark_Tri(), SUMA_MarkLineSurfaceIntersect(), SUMA_MaskDsetByClustList(), SUMA_MaskOfNodesInPatch(), SUMA_mattoquat(), SUMA_MemberFaceSets(), SUMA_Mesh_Area(), SUMA_Mesh_IJK2Mesh_IJK_nel(), SUMA_Mesh_IJK_nel2Mesh_IJK(), SUMA_Mesh_Resample(), SUMA_Mesh_Volume(), SUMA_MeshAxisStandard(), SUMA_Message_destroyed(), SUMA_Message_open(), SUMA_MixColors(), SUMA_MixOverlays(), SUMA_momentum(), SUMA_morphToStd(), SUMA_MovePlaneDown(), SUMA_MovePlaneUp(), SUMA_MT_intersect_triangle(), SUMA_MT_isIntersect_Triangle(), SUMA_nel_stdout(), SUMA_New_Additions(), SUMA_New_Additions_perver(), SUMA_New_FormAfniDset_Opt(), SUMA_New_ViewState(), SUMA_NewAreaAtRadius(), SUMA_NewDsetGrp(), SUMA_NewDsetID(), SUMA_NewDsetPointer(), SUMA_NewGeometryInViewer(), SUMA_NewM2M(), SUMA_NewNel(), SUMA_NewNewSOOpt(), SUMA_NewSO(), SUMA_NewSurfaceGeometry(), SUMA_NewVolumeAtRadius(), SUMA_Next_Best_Seed(), SUMA_NextState(), SUMA_NI_decode_string_list(), SUMA_NI_get_ith_string(), SUMA_NI_str_ar_2_comp_str(), SUMA_niml_call(), SUMA_niml_hangup(), SUMA_niml_workproc(), SUMA_NIMLDrawnROI_to_DrawnROI(), SUMA_nimlSO2SO(), SUMA_NN_GeomSmooth(), SUMA_NodeInput(), SUMA_NodePath_to_EdgePath(), SUMA_NodePath_to_TriPath_Inters(), SUMA_NodePath_to_TriPath_Inters_OLD(), SUMA_NodesInROI(), SUMA_NodeVal2irgba_nel(), SUMA_NodeXYZ2NodeXYZ_nel(), SUMA_NodeXYZ_nel2NodeXYZ(), SUMA_oDsetNel2nDsetNgr(), SUMA_Offset_GeomSmooth(), SUMA_ok_orstring(), SUMA_OKassign(), SUMA_OpenDrawnROI(), SUMA_OpenDrawnROI_1D(), SUMA_OpenDrawnROI_NIML(), SUMA_OpenDrawROIWindow(), SUMA_OpenDX2dset(), SUMA_OpenDx_Object_Attr(), SUMA_OpenDx_Object_Components(), SUMA_OpenDx_Object_Data(), SUMA_OpenDx_Object_Header_Field(), SUMA_OpenDX_Read(), SUMA_OpenDX_Read_CruiseVolHead(), SUMA_OpenDX_Read_SO(), SUMA_OpenDX_Write(), SUMA_OpenGLStateReset(), SUMA_optmenu_EV(), SUMA_orcode_to_orstring(), SUMA_OrientTriangles(), SUMA_originto3d_2_originHEAD(), SUMA_orstring_to_orcode(), SUMA_Overlays_2_GLCOLAR4(), SUMA_OverlaysToOrderedList(), SUMA_pad_str(), SUMA_pad_string(), SUMA_Paint_SO_ROIplanes(), SUMA_Paint_SO_ROIplanes_w(), SUMA_ParseFname(), SUMA_ParseInput_basics(), SUMA_ParseLHS_RHS(), SUMA_Patch2Surf(), SUMA_Pattie_Volume(), SUMA_PercRange(), SUMA_Plane_Equation(), SUMA_PlaneOrder_Info(), SUMA_Ply_Read(), SUMA_Ply_Write(), SUMA_Point_At_Distance(), SUMA_Point_To_Line_Distance(), SUMA_Point_To_Point_Distance(), SUMA_PolySurf3(), SUMA_PopUpMessage(), SUMA_PositionWindowRelative(), SUMA_postRedisplay(), SUMA_Prefix2SurfaceName(), SUMA_PrepAddmappableSO(), SUMA_PrependToROIdatum(), SUMA_PrepSO_GeomProp_GL(), SUMA_PrevState(), SUMA_Print_PlaneOrder(), SUMA_Print_Surface_Object(), SUMA_process_environ(), SUMA_process_NIML_data(), SUMA_ProcessBrushStroke(), SUMA_PROGRAM_NAME_ParseInput(), SUMA_ProjectSurfaceToSphere(), SUMA_PromptActivate_cb(), SUMA_PromptApply_cb(), SUMA_PromptButtonLabel(), SUMA_PromptCancel_cb(), SUMA_PromptClear_cb(), SUMA_PromptHelp_cb(), SUMA_PromptOk_cb(), SUMA_PromptUnmap_cb(), SUMA_qhull_wrap(), SUMA_quit_timeout_CB(), SUMA_RangeTableCell_EV(), SUMA_read1D(), SUMA_Read_2Ddfile(), SUMA_Read_2Dfile(), SUMA_Read_dfile(), SUMA_Read_file(), SUMA_Read_IRGB_file(), SUMA_read_ppm(), SUMA_Read_SpecFile(), SUMA_Read_SureFit_Param(), SUMA_ReadCharStdin(), SUMA_readColor(), SUMA_readFSannot(), SUMA_readFScurv(), SUMA_ReadNumStdin(), SUMA_ReadSegDO(), SUMA_Recycle_getoffsets(), SUMA_RedisplayAllShowing(), SUMA_RefreshDsetList(), SUMA_register_workproc(), SUMA_RegisterCommand(), SUMA_RegisterDO(), SUMA_RegisteredSOs(), SUMA_RegisterEngineData(), SUMA_RegisterEngineListCommand(), SUMA_RegisterGroup(), SUMA_RegisterMessage(), SUMA_RegisterSpecSO(), SUMA_ReleaseActionStackData(), SUMA_ReleaseEngineData(), SUMA_ReleaseEngineListElement(), SUMA_ReleaseLink(), SUMA_ReleaseMessageListElement(), SUMA_ReleaseOverlay(), SUMA_RemixRedisplay(), SUMA_remove_workproc(), SUMA_remove_workproc2(), SUMA_RemoveCoordBias(), SUMA_RemoveDO(), SUMA_RemoveDsetExtension(), SUMA_RemoveSO_CoordBias(), SUMA_RemoveSurfNameExtension(), SUMA_RenderToPixMap(), SUMA_reorder(), SUMA_ReportDrawnROIDatumLength(), SUMA_Reposition_Touchup(), SUMA_resize(), SUMA_response(), SUMA_ROIv2dataset(), SUMA_ROIv2Grpdataset(), SUMA_SampBias_ParseInput(), SUMA_Save_Surface_Object(), SUMA_SaveDrawnROI(), SUMA_SaveDrawnROI_1D(), SUMA_SaveDrawnROINIML(), SUMA_SaveSOascii(), SUMA_SaveVisualState(), SUMA_ScaleToMap(), SUMA_ScaleToMap_alaAFNI(), SUMA_ScaleToMap_Interactive(), SUMA_ScaleToMapOpt_Info(), SUMA_ScaleToMapOptInit(), SUMA_sdset_id(), SUMA_sdset_idmdom(), SUMA_Search_Min_Dist(), SUMA_SendDset_Afni(), SUMA_SendSumaNewSurface(), SUMA_SendToAfni(), SUMA_SendToSuma(), SUMA_set_cmap_options(), SUMA_set_Lock_arb(), SUMA_set_Lock_rb(), SUMA_set_LockView_atb(), SUMA_set_string_length(), SUMA_SetAllRemixFlag(), SUMA_SetCellEditMode(), SUMA_SetCmapMenuChoice(), SUMA_SetConvexityPlaneDefaults(), SUMA_SetCoordBias(), SUMA_SetcSV(), SUMA_SetLight0(), SUMA_SetLocalRemixFlag(), SUMA_SetNumForeSmoothing(), SUMA_SetRangeTableTit_EV(), SUMA_SetRangeValue(), SUMA_SetRemixFlag(), SUMA_SetScaleRange(), SUMA_SetScaleThr(), SUMA_SetShownLocalRemixFlag(), SUMA_SetSO_CoordBias(), SUMA_SetSVForegroundColor(), SUMA_SetupSVforDOs(), SUMA_Show_ColorOverlayPlanes(), SUMA_Show_CommonFields(), SUMA_Show_DOv(), SUMA_Show_Edge_List(), SUMA_Show_FreeSurfer(), SUMA_Show_FS_ColorTable(), SUMA_Show_IO_args(), SUMA_Show_MT_intersect_triangle(), SUMA_Show_NI_str_ar(), SUMA_Show_OpenDX_Struct(), SUMA_Show_SO_map(), SUMA_Show_SPI(), SUMA_show_STB(), SUMA_Show_SureFit(), SUMA_Show_SurfaceViewer_Struct(), SUMA_Show_SurfClust_list(), SUMA_Show_SurfClust_list_Info(), SUMA_Show_ViewState(), SUMA_Show_VolPar(), SUMA_ShowAllVisuals(), SUMA_ShowBrushStroke(), SUMA_ShowDrawnROI(), SUMA_ShowDrawnROIDatum(), SUMA_ShowDset(), SUMA_ShowList(), SUMA_ShowMemTrace(), SUMA_ShowMeSome(), SUMA_ShowMeTheChildren(), SUMA_ShowNel(), SUMA_ShowOffset_Info(), SUMA_ShowOffset_ll_Info(), SUMA_ShowPatch(), SUMA_ShowScaleToMapOpt(), SUMA_ShowSpecStruct(), SUMA_ShowVisual(), SUMA_SizeOf(), SUMA_sizeto3d_2_deltaHEAD(), SUMA_SmoothAttr_Neighb(), SUMA_SmoothAttr_Neighb_Rec(), SUMA_SO2nimlSO(), SUMA_SOGroup_2_Spec(), SUMA_SortedAxisSegmentList(), SUMA_sources_Info(), SUMA_SOVolPar2VolPar_nel(), SUMA_SpecStructInfo(), SUMA_Sph2Cart(), SUMA_SphereQuality(), SUMA_StandardMapCode(), SUMA_StandardMapName(), SUMA_StretchToFitLeCerveau(), SUMA_StringAppend(), SUMA_StringAppend_va(), SUMA_StringToNum(), SUMA_StripPath(), SUMA_Subdivide_Mesh(), SUMA_suck_file(), SUMA_Suggest_Touchup(), SUMA_Suggest_Touchup_Grad(), SUMA_SumaInfo_destroyed(), SUMA_SumaInfo_open(), SUMA_SureFit_Read_Coord(), SUMA_SureFit_Read_Topo(), SUMA_SureFit_Write(), SUMA_Surf_Plane_Intersect(), SUMA_Surf_Plane_Intersect_ROI(), SUMA_Surface_Curvature(), SUMA_SurfaceFileName(), SUMA_SurfaceMetrics(), SUMA_SurfaceMetrics_eng(), SUMA_SurfaceObject_Info(), SUMA_SurfaceTypeCode(), SUMA_SurfaceTypeString(), SUMA_SurfaceViewer_StructInfo(), SUMA_SurfClust_list_2_DsetMask(), SUMA_SurfGridIntersect(), SUMA_SurfInfo_destroyed(), SUMA_SurfInfo_open(), SUMA_SurfNorm(), SUMA_SurfToSurf_ParseInput(), SUMA_SwitchColPlaneCmap(), SUMA_SwitchGroups(), SUMA_SwitchState(), SUMA_TableF_cb_label_change(), SUMA_TableF_cb_label_Modify(), SUMA_TableF_SetString(), SUMA_Take_A_Hike(), SUMA_Taubin_Smooth(), SUMA_Taubin_Smooth_Coef(), SUMA_Taubin_Smooth_TransferFunc(), SUMA_tesselate(), SUMA_THD_3dfind_to_3dmm(), SUMA_THD_3dind_to_3dmm(), SUMA_THD_3dmm_to_3dfind(), SUMA_THD_3dmm_to_3dind(), SUMA_THD_3dmm_to_dicomm(), SUMA_THD_dicomm_to_3dmm(), SUMA_ThreshVal2ScalePos(), SUMA_TransferCoordBias(), SUMA_TransferSO_CoordBias(), SUMA_triangulateRow(), SUMA_TriInput(), SUMA_TriNorm(), SUMA_TriSurf3(), SUMA_TriSurf3v(), SUMA_truncate_string(), SUMA_TypeOfColNumb(), SUMA_TypeOfDsetColNumb(), SUMA_UndoAction(), SUMA_UniqueInt(), SUMA_UniqueInt_ind(), SUMA_UnlinkFromPointer(), SUMA_UnRegisterDO(), SUMA_unSetcSV(), SUMA_UpdateAllViewerCursor(), SUMA_UpdateColPlaneShellAsNeeded(), SUMA_UpdateNodeField(), SUMA_UpdateNodeLblField(), SUMA_UpdateNodeNodeField(), SUMA_UpdateNodeValField(), SUMA_UpdateRotaCenter(), SUMA_UpdateScrolledListData(), SUMA_UpdateTriField(), SUMA_UpdateViewerCursor(), SUMA_UpdateViewerTitle(), SUMA_UpdateViewerTitle_old(), SUMA_UpdateViewPoint(), SUMA_UpdateXhairField(), SUMA_VarType2ColType(), SUMA_VarType2TypeCast(), SUMA_vec_3dfind_to_3dmm(), SUMA_vec_3dfind_to_dicomm(), SUMA_vec_3dmm_to_3dfind(), SUMA_vec_3dmm_to_dicomm(), SUMA_vec_dicomm_to_3dfind(), SUMA_vec_dicomm_to_3dmm(), SUMA_VEC_Read(), SUMA_VEC_Write(), SUMA_Version(), SUMA_ViewerInfo_destroyed(), SUMA_ViewerInfo_open(), SUMA_ViewStateInfo(), SUMA_VisibleSOs(), SUMA_VolDiff(), SUMA_VolDims(), SUMA_VolPar_Attr(), SUMA_VolPar_Info(), SUMA_VolPar_nel2SOVolPar(), SUMA_VolParFromDset(), SUMA_VoxelNeighbors(), SUMA_VoxelsInBox(), SUMA_WhatAreYouToMe(), SUMA_which_stream_index(), SUMA_whichDO(), SUMA_WhichGroup(), SUMA_WhichState(), SUMA_WhichSV(), SUMA_whichTri(), SUMA_WhichViewerInMomentum(), SUMA_WidgetResize(), SUMA_workprocess(), SUMA_World2ScreenCoords(), SUMA_WorldAxisStandard(), SUMA_write1D(), SUMA_Write_DrawnROI_1D(), SUMA_Write_DrawnROI_NIML(), SUMA_writeColorFile(), SUMA_WriteDset(), SUMA_writeFSfile(), SUMA_writeSpecFile(), SUMA_X_SurfaceViewer_Create(), SUMA_XhairInput(), SUMA_XYZ_XYZmap(), SUMA_XYZmap_XYZ(), SUMA_z_doubqsort(), SUMA_z_dqsort(), SUMA_z_dqsort_nsc(), SUMA_z_qsort(), SumaToGts(), usage_3dBRAIN_VOYAGERtoAFNI(), usage_3dCRUISEtoAFNI(), usage_3dSurfMask(), usage_PROGRAM_NAME(), usage_SUMA_coarsen(), usage_SUMA_SampBias(), and usage_SurfToSurf().

function[err, maplocation, mapsign, Mtrans]
 

Initial value:

 AFNI_CoordChange (Orig, Trans, Morig)
%
%   [err, maplocation, mapsign, Mtrans] = AFNI_CoordChange (Orig, Trans, [Morig])
%
%Purpose:
%   Change the AFNI coordinate system between the 48 different coordinate systems allowed
%   Coordinates are as they appear on the top left corner of AFNI's controller
%   Coord Order plugin is used to change the coordinate system in AFNI
%   
%Input Parameters:
%   Orig : the 1x3 letter or number code for the original orientation

Definition at line 1 of file AFNI_CoordChange.m.

Referenced by main(), and ReadParamFile().

end itmp = find (OrCode == TrCode(i))
 

Definition at line 89 of file AFNI_CoordChange.m.

end maplocation = [0 0 0]
 

mapsign = [0 0 0]
 

Morig = []
 

Definition at line 50 of file AFNI_CoordChange.m.

Mtrans
 

Initial value:

 AFNI_CoordChange ('RAI', 'ALI', [1 2 3; 4 5 6])
%
%     Author : Ziad Saad
%     Date : Tue Sep 5 18:56:40 PDT 2000
%     LBC/NIMH/ National Institutes of Health

else OrCode = AFNI_OrientCode (Orig) Orig
 

Definition at line 68 of file AFNI_CoordChange.m.

else look for opposite orientation
 

Definition at line 83 of file AFNI_CoordChange.m.

end return
 

Definition at line 396 of file WriteBrik.m.

Referenced by AB_interp(), absfft_func(), add_extra_color(), add_open_stream(), add_tracker(), add_TRUST_host(), add_trusted_host(), addto_args(), addto_Dtable(), addto_Htable(), AFNI_add_interruptable(), AFNI_broutim_CB(), AFNI_concatenate_warp(), AFNI_decode_geom(), AFNI_dicomm_to_xyz(), AFNI_do_bkgd_lab(), AFNI_exit(), AFNI_get_xhair_node(), AFNI_handler(), AFNI_ijk_to_xyz(), AFNI_make_descendants(), AFNI_mark_environ_done(), AFNI_niml_atexit(), AFNI_niml_driver(), AFNI_plugout_exit(), AFNI_pop_whereami_kill(), AFNI_popup_message(), AFNI_popup_sonnet(), AFNI_process_interrupts(), AFNI_range_setter(), AFNI_register_nD_func_init(), AFNI_register_nD_function(), AFNI_see_ttatlas_CB(), AFNI_send_image(), AFNI_serverlog(), AFNI_sleep(), AFNI_sonnet_CB(), AFNI_splashraise(), AFNI_start_io(), AFNI_start_version_check(), AFNI_store_dset_index(), AFNI_view_setter(), AFNI_xyz_to_dicomm(), AFNI_xyz_to_ijk(), AIVVV_imseq_retitle(), AIVVV_imseq_send_CB(), alter_PLUGIN_strval_width(), AP_press_CB(), AP_timer_CB(), append_string_to_args(), append_to_memplot(), appendto_string_list(), apply_3shear(), apply_xshear(), apply_yshear(), apply_zshear(), AREN_be_quiet(), AREN_be_verbose(), AREN_set_size(), AREN_set_viewpoint(), atexit_open_streams(), atr_print(), auto_grid(), AV_assign_fval(), AV_fval_to_char(), AV_leave_EV(), AV_press_CB(), AV_timer_CB(), AVOPT_press_CB(), B2F_read_opts(), B64_set_crlf(), B64_set_linelen(), B64_to_base64(), B64_to_binary(), backward_solve_inplace(), basis_write_iresp(), basis_write_sresp(), beep_CB(), beta_init(), blanktrim(), BUCK_read_opts(), CALC_read_opts(), cfft2d(), check_xrestore_data(), CL_read_opts(), clustedit3D(), collapse_illegals(), collapse_xy(), compute_choleski(), conv_model(), conv_set_ref(), CREN_dset_axes(), CREN_set_angles(), CREN_set_axes(), CREN_set_databytes(), CREN_set_interp(), CREN_set_min_opacity(), CREN_set_opamap(), CREN_set_render_mode(), CREN_set_rgbmap(), CREN_set_rotaxes(), CREN_set_skewmat(), CREN_set_viewpoint(), crush(), csfft(), csfft_cox(), csfft_many(), csfft_print(), csfft_trigconsts(), cub_shift2(), cutlines_memplot(), DC_bg_color(), DC_color_bright(), DC_color_squeeze(), DC_fg_color(), DC_fg_colorpix(), DC_fg_colortext(), DC_gray_change(), DC_gray_conbrio(), DC_gray_contrast(), DC_init_im_col(), DC_init_im_gry(), DC_linestyle(), DC_linewidth(), DC_palette_rotate(), DC_palette_setcolor(), DC_palette_setgray(), DC_palette_swap(), DC_pixel_to_rgb(), DC_rgb_to_ovrgb(), DC_set_image_colors(), DC_yokify(), decode_geom(), DELAY_tsfuncV2(), delete_active_memplot(), delete_memplot(), destroy_AREN_renderer(), destroy_CREN_renderer(), destroy_Dtable(), destroy_header_stuff(), destroy_Htable(), destroy_MREN_colortable(), destroy_MREN_renderer(), destroy_PLUGIN_strval(), detrend(), do_xrestore_stuff(), donebut_CB(), DRAW_2D_circle(), DRAW_2D_expand(), draw_2dfiller(), DRAW_2dfiller(), DRAW_3D_expand(), DRAW_3D_sphere(), DRAW_attach_dtable(), DRAW_choose_CB(), DRAW_collapsar(), DRAW_color_CB(), DRAW_copy_bbox_CB(), DRAW_done_CB(), DRAW_fillin_CB(), DRAW_finalize_dset_CB(), DRAW_help_CB(), DRAW_label_CB(), DRAW_label_EV(), DRAW_label_finalize(), DRAW_label_getfile(), DRAW_make_widgets(), DRAW_mode_CB(), DRAW_quit_CB(), DRAW_receiver(), DRAW_redo_CB(), DRAW_save_CB(), DRAW_saveas_CB(), DRAW_saveas_finalize_CB(), DRAW_set_value_label(), DRAW_ttatlas_CB(), DRAW_undo_butlab(), DRAW_undo_CB(), DRAW_undo_sizecheck(), DRAW_value_CB(), draw_xseg(), drawGraf(), DrawSubWindow(), DT_read_opts(), dump_vallab(), duplicate_string_list(), EDIT_add_brick(), EIG_tsfunc(), elvis_CB(), enable_mcw_malloc(), ENV_add_numeric(), ENV_add_string(), ENV_globalrange(), ENV_sesstrail(), estpdf_float(), evaluate_bitvec(), evolve_bitvector_array(), exit_me_baby(), EXP0D_worker(), expose_CB(), extract_assign_directions(), extract_byte_fs(), extract_byte_liby(), extract_byte_lifl(), extract_byte_lix(), extract_byte_lixx(), extract_byte_nn(), extract_byte_speedtest(), extract_byte_ts(), extract_byte_tsx(), extract_rgba_nn(), EXTRACT_tsfunc(), F1D_chainfunc(), F2D_chainfunc(), fd_line(), fd_txt(), fft128(), fft16(), fft256(), fft2D_func(), fft32(), fft512(), fft64(), fft8(), FFT_1dcx(), FFT_2dchirpz(), FFT_2dcx(), fft_3dec(), fft_4dec(), fft_5dec(), find_base_value(), find_unusual_correlations(), fix_bitvector(), fix_bitvector_piece(), flip(), flip180(), flip90(), flip_memplot(), flip_xy(), flip_xz(), flip_yz(), forward_solve_inplace(), fred_CB(), free_PCOR_references(), free_PCOR_voxel_corr(), free_references(), free_string_list(), free_Tmask(), free_track(), free_voxel_corr(), freeup_strings(), ft_shift2(), ft_xshear(), ft_yshear(), FTOSH_getopts(), gamma_model(), gaussians(), ge_header(), get_best_shift(), get_coef(), get_laguerre_table(), get_line_opt(), get_linear_trend(), get_lsqfit(), get_pcor(), get_pcor_thresh_coef(), get_quadratic_trend(), get_siemens_extra_info(), get_variance(), getplane_byte(), GRA_overlay_circle(), GRA_small_circle(), GRA_winavertimer_CB(), GRAF_curve_CB(), GRAF_drawing_EV(), GRAF_get_setup(), GRAF_handle_CB(), GRAF_pasdrawing_EV(), GRAF_put_setup(), GRAF_reset_CB(), GRAF_set_func(), GRAF_set_xyrange(), graf_state_get(), graf_state_put(), GRAPH_find_components(), grid_down(), grid_up(), handle_tta(), hept_shift2(), HI_read_opts(), hidden_NI_free(), huber_func(), ibeta(), init_AREN_colortable(), init_bitvector_array(), init_colors(), init_floatvector_array(), init_histo(), init_MCW_sizes(), init_MREN_colortable(), init_registry(), init_TRUST_list(), init_trusted_list(), init_XDBE(), input_CB(), insert_at_memplot(), INTERP_destroy(), INTERP_evaluate(), invert2d(), invert_bitvector(), invert_bitvector_piece(), iochan_close(), iochan_set_cutoff(), iochan_sleep(), isort_double(), isort_doubleint(), isort_float(), isort_floatfloat(), isort_floatint(), isort_floatstuff(), isort_int(), isort_intint(), ISORT_NAME(), isort_pair(), isort_sh(), isort_short(), ISQ_butsave_choice_CB(), ISQ_butsave_EV(), ISQ_opacity_CB(), ISQ_place_dialog(), ISQ_redisplay(), ISQ_set_cursor_state(), ISQ_setup_ppmto_filters(), ISQ_show_bar(), ISQ_show_image(), JPEG_matrix_gray(), kill_graph_xy(), L1F_detrend(), L1F_fitter(), L1F_worker(), lacy9_box_func(), lin_shift2(), line_color(), linear3_func(), linear_filter_extend(), linear_filter_trend(), linear_filter_zero(), linear_reg(), load_decode_table(), load_encode_table(), load_tmp_colors(), log10_func(), LSQ_detrend(), LSQ_fitter(), LSQ_worker(), make_plot(), mangle_angle(), mat_down(), mat_up(), MCW_alter_widget_cursor(), MCW_bbox_hints(), MCW_choose_editable_strlist(), MCW_choose_strlist(), MCW_click_help_CB(), MCW_discard_events(), MCW_expose_widget(), MCW_fc7(), MCW_file_expand(), mcw_free(), MCW_free_expand(), MCW_hash_idcode(), MCW_help_CB(), MCW_hint_toggle(), MCW_histo_bytes(), MCW_intlist_allow_negative(), MCW_invert_widget(), MCW_list_mode_CB(), mcw_malloc_dump(), MCW_manage_widgets(), MCW_popdown_meter(), MCW_reghelp_children(), MCW_reghint_children(), MCW_register_help(), MCW_register_hint(), MCW_set_colormap(), MCW_set_listmax(), MCW_set_meter(), MCW_set_widget_bg(), MCW_set_widget_cursor(), MCW_textwin_CB(), MCW_textwinkill_CB(), MCW_unhelp_CB(), MCW_unmanage_widgets(), MCW_unregister_hint(), MCW_widget_geom(), MCW_wildcards(), mcw_XtFree(), median21_box_func(), median3_func(), median9_box_func(), memplot_to_postscript(), memplot_to_X11_sef(), merge_cohar(), move(), mpeg_setup(), MREN_be_quiet(), MREN_be_verbose(), MREN_depth_cue(), MREN_set_min_opacity(), MREN_set_precalculation(), MREN_set_rgbmap(), MREN_set_size(), MREN_set_viewpoint(), MREN_unset_rgbmap(), mri_2dalign_cleanup(), mri_2dalign_method(), mri_2dalign_params(), mri_3dalign_blurring(), mri_3dalign_final_regmode(), mri_3dalign_method(), mri_3dalign_params(), mri_align_method(), mri_align_params(), mri_edgize(), mri_fft_complex(), mri_fix_data_pointer(), mri_input_delay(), mri_percents(), mri_purge_delay(), mri_swap2(), mri_swap4(), mri_warp3D_align_cleanup(), mri_warp3D_get_delta(), MTD_killfunc(), multivector_free(), multivector_set_name(), MV_fval_to_char(), NI_add_column(), NI_add_column_stride(), NI_add_to_group(), NI_add_trusted_host(), NI_alter_veclen(), NI_convert_elm_to_obj(), NI_dpr(), NI_fill_column_stride(), NI_free_column(), NI_free_element(), NI_free_struct(), NI_fval_to_char(), NI_insert_string(), NI_insert_value(), NI_malloc_dump(), NI_malloc_enable_tracking(), NI_register_doer(), NI_register_objconverters(), NI_register_struct(), NI_registry_free(), NI_registry_idcode_altername(), NI_registry_ptr_altername(), NI_registry_ptr_to_idcode(), NI_registry_ptr_to_len(), NI_registry_ptr_to_name(), NI_remove_from_group(), NI_rename_group(), NI_reset_buffer(), NI_set_attribute(), NI_set_axes(), NI_set_delta(), NI_set_dimen(), NI_set_origin(), NI_set_units(), NI_set_vector_range(), NI_sleep(), NI_stat_decode(), NI_stream_clearbuf(), NI_stream_close(), NI_stream_close_keep(), NI_stream_closenow(), NI_stream_kill(), NI_stream_seek(), NI_stream_setbuf(), NI_suck_stream(), NI_swap2(), NI_swap4(), NI_swap8(), NI_swap_column(), NI_unregister_struct(), nifti_set_afni_extension(), niml_to_intvec(), niml_to_matrix(), NIML_to_stderr(), niml_to_stringvec(), niml_to_symvec(), NL_error(), NL_fitter(), NL_worker(), nn_shift2(), nonmax_kill(), normalize(), normalize_doublevector(), normalize_floatvector(), NOTES_add_CB(), NOTES_choose_CB(), NOTES_delete_CB(), NOTES_done_CB(), NOTES_finalize_dset_CB(), NOTES_help_CB(), NOTES_make_widgets(), NOTES_quit_CB(), NOTES_refit_CB(), NOTES_restore_CB(), NOTES_save_CB(), NUD_brick_av_CB(), NUD_choose_CB(), NUD_clear_CB(), NUD_doall_CB(), NUD_finalize_dset_CB(), NUD_help_CB(), NUD_make_widgets(), NUD_nudge_CB(), NUD_print_CB(), NUD_quit_CB(), NUD_redo_CB(), NUD_rotate(), NUD_setcumlab(), NUD_undo_CB(), NUD_undopush(), NUD_update_base(), one_bitvector(), one_bitvector_piece(), optmenu_EV(), osfilt3_func(), osfilt9_box_func(), outer9_box_func(), OVC_mostest(), overlay_txt(), PARSER_evaluate_vector(), PARSER_mark_symbols(), PASGRAF_set_xyrange(), PBAR_labelize(), PC_read_opts(), PCOR_get_coef(), PCOR_get_lsqfit(), PCOR_get_mcor(), PCOR_get_pcor(), PCOR_get_pcor_and_coef(), PCOR_get_perc(), PCOR_get_stdev(), PCOR_get_variance(), PCOR_UPDATE(), PDF_sprint(), pfit(), PH_redraw(), PH_startup_timeout_CB(), plot_fdX(), plot_line(), plot_strip_addto(), plot_strip_clear(), plot_ts_addto(), plot_ts_lab(), plot_ts_qqq(), plotcirc_memplot(), plotkill_topshell(), plotline_memplot(), plotpak_getset(), plotpak_srface(), plotrect_memplot(), PLUGIN_seq_send_CB(), PLUTO_beep(), PLUTO_imseq_addto(), PLUTO_imseq_destroy(), PLUTO_imseq_rekill(), PLUTO_imseq_retitle(), PLUTO_imseq_send_CB(), PLUTO_imseq_setim(), PLUTO_report(), PLUTO_set_runlabels(), ppak_garbage_routine(), PR_one_slice(), prepend_string_to_args(), probe_track(), proc_finalize_shm_volumes(), proc_free(), Process_Options(), profile_Htable(), project_byte_mip(), ps_move(), pscancel_CB(), psfile_CB(), psfinalize_CB(), psprint_CB(), putin_fop_table(), putplane_byte(), qmedmad_float(), qsort_double(), qsort_doubleint(), qsort_float(), qsort_floatfloat(), qsort_floatint(), qsort_floatstuff(), qsort_int(), qsort_intint(), qsort_pair(), qsort_short(), qsrec_double(), qsrec_doubleint(), qsrec_float(), qsrec_floatfloat(), qsrec_floatint(), qsrec_floatstuff(), qsrec_int(), qsrec_intint(), QSREC_NAME(), qsrec_pair(), qsrec_sh(), qsrec_short(), quadrant_fimfunc(), quint_shift2(), RAN_setup(), randomize_bitvector(), randomize_bitvector_piece(), rank_order_float(), RCREND_accum_lab_CB(), RCREND_done_CB(), RCREND_done_timeout_CB(), read_ascii_floats(), redraw_MCW_pasgraf(), redraw_topshell(), REG_command_line(), REG_syntax(), remove_isolated_stuff(), remove_open_stream(), removefrom_Dtable_a(), removefrom_Dtable_b(), removefrom_Htable(), REND_accum_CB(), REND_angle_CB(), REND_autocancel_CB(), REND_autocompute_CB(), REND_autoflag_CB(), REND_choose_av_CB(), REND_choose_CB(), REND_clip_CB(), REND_clusters_av_CB(), REND_color_bbox_CB(), REND_color_opacity_CB(), REND_color_pbar_CB(), REND_colornum_av_CB(), REND_cut_overlay_CB(), REND_cutout_blobs(), REND_cutout_set_CB(), REND_cutout_type_CB(), REND_destroy_imseq(), REND_do_incrot(), REND_done_CB(), REND_done_timeout_CB(), REND_draw_CB(), REND_dynamic_CB(), REND_environ_CB(), REND_finalize_dset_CB(), REND_finalize_func_CB(), REND_func_widgets(), REND_graf_CB(), REND_help_CB(), REND_inc_angles(), REND_incrot_CB(), REND_init_cmap(), REND_kill_clusters_CB(), REND_load_cutout_state(), REND_load_dsl(), REND_make_widgets(), REND_mixshade_av_CB(), REND_numcutout_CB(), REND_opacity_scale_CB(), REND_open_func_CB(), REND_open_imseq(), REND_overlay_ttatlas(), REND_palette_av_CB(), REND_pbarmenu_CB(), REND_pbarmenu_EV(), REND_precalc_CB(), REND_range_av_CB(), REND_range_bbox_CB(), REND_read_exec_CB(), REND_read_this_CB(), REND_read_this_finalize_CB(), REND_reload_CB(), REND_reload_dataset(), REND_reload_func_dset(), REND_reload_renderer(), REND_rotmatrix_to_angles(), REND_save_many_CB(), REND_save_this_CB(), REND_script_brindex_CB(), REND_script_CB(), REND_script_dset_CB(), REND_script_graf_CB(), REND_script_load_CB(), REND_script_menu(), REND_see_overlay_CB(), REND_see_ttatlas_CB(), REND_seq_send_CB(), REND_set_pbar_top_CB(), REND_set_thr_pval(), REND_setup_color_pbar(), REND_state_to_widgets(), REND_textact_CB(), REND_thr_scale_CB(), REND_thr_scale_drag_CB(), REND_thresh_top_CB(), REND_update_imseq(), REND_widgets_to_state(), REND_xhair_CB(), REND_xhair_EV(), REND_xhair_overlay(), REND_xhair_recv(), REND_xhair_underlay(), resize_CB(), resize_Htable(), rotangles(), RT_check_info(), RT_exit(), RT_finish_dataset(), RT_image_kfun(), RT_process_image(), RT_process_xevents(), RT_read_image(), RT_registration_2D_atend(), RT_registration_2D_close(), RT_registration_2D_onevol(), RT_registration_2D_realtime(), RT_registration_2D_setup(), RT_registration_3D_atend(), RT_registration_3D_close(), RT_registration_3D_onevol(), RT_registration_3D_realtime(), RT_registration_3D_setup(), RT_start_child(), RT_start_dataset(), RT_startup(), RT_tell_afni(), RT_tell_afni_one(), RWC_destroy_nullify(), RWC_destroy_nullify_cancel(), RWC_init_fim_colors(), RWC_medfilt_time_series(), RWC_setup_fims(), RWC_sleep(), RWC_visibilize_CB(), RWC_XtPopdown(), RWCOX_popper(), save_ppm(), scale_down(), scale_memplot(), scale_up(), scroll_timeout_CB(), scroll_topbot(), SEGMENT_auto(), SER_destroy_vector(), SER_free_vector(), set_color_memplot(), set_MCW_pasgraf(), set_opacity_memplot(), set_PLUGIN_strval(), set_thick_memplot(), set_unusuality_tail(), set_URL_ftp_ident(), set_X11_background(), setup_basic_types(), setup_byper(), setup_tmpdir(), setup_X11_plotting(), SFIM_getopts(), SHIFT_set_method(), SHIFT_two_rows(), shiftdeltas(), SHM_close(), sin_func(), sin_grad(), SNAP_warnhandler(), sort_shortvox(), spearman_fimfunc(), ssqrt_func(), startup_timeout_CB(), STATS_tsfunc(), subsume_Htable(), SUMA_destroy_vnlist(), svd_double(), swaptest(), symeig_double(), symeigval_double(), T3D_data_to_widgets(), T3D_imseq_CB(), T3D_open_view_CB(), T3D_pointer_leave_EV(), T3D_quit_CB(), T3D_save_file_CB(), T3D_stat_aux_CB(), T3D_type_av_CB(), T3D_voxshape_CB(), T3D_widgets_to_data(), TAG_add_CB(), TAG_beep_CB(), TAG_clear_CB(), TAG_clearall_CB(), TAG_columnize(), TAG_copy_CB(), TAG_delete_CB(), TAG_done_CB(), TAG_dset_CB(), TAG_get_copy_CB(), TAG_get_dset_CB(), TAG_help_CB(), TAG_make_widgets(), TAG_onoff(), TAG_quit_CB(), TAG_read_CB(), TAG_redraw(), TAG_relabel_CB(), TAG_reset_widgets(), TAG_save_CB(), TAG_set_CB(), TAG_tog_CB(), TAG_value_CB(), TAG_write_CB(), TCAT_read_opts(), tcp_set_cutoff(), tcp_sigurg_handler(), TFIM_getopts(), THD_3mni_to_3tta(), THD_3tta_to_3mni(), THD_append_datablock_keywords(), THD_append_dataset_keywords(), THD_const_detrend(), THD_coorder_fill(), THD_coorder_to_dicom(), THD_copy_datablock_auxdata(), THD_cubic_detrend(), THD_delete_diskptr(), THD_dicom_to_coorder(), THD_edit_dataxes(), THD_enviro_write_order(), THD_erase_all_atr(), THD_erase_one_atr(), THD_force_malloc_type(), THD_generic_detrend(), THD_init_datablock_keywords(), THD_init_datablock_labels(), THD_init_datablock_stataux(), THD_insert_series(), THD_linear_detrend(), THD_load_statistics(), THD_mask_clust(), THD_mask_dilate(), THD_mask_erode(), THD_normalize(), THD_quadratic_detrend(), THD_rota_envpad(), THD_rota_method(), THD_rota_setpad(), THD_rota_vol_2byte(), THD_rota_vol_byte(), THD_rota_vol_matvec(), THD_rota_vol_matvec_2byte(), THD_set_storage_mode(), THD_set_write_compression(), THD_set_write_order(), THD_store_datablock_keywords(), THD_store_datablock_label(), THD_store_datablock_stataux(), THD_store_dataset_keywords(), THD_unzblock(), THD_update_one_bstat(), THD_update_statistics(), THD_write_nimlatr(), THD_zblock(), tokenize_string(), tross_Add_Note(), tross_Addto_History(), tross_Append_History(), tross_Copy_History(), tross_Delete_Note(), tross_Dont_Encode_Slash(), tross_Make_History(), tross_multi_Append_History(), tross_Replace_History(), tross_Store_Note(), TRUST_addhost(), ts_shift(), ts_shift2(), ts_shift_2byte(), TT_purge_atlas(), TT_purge_atlas_big(), TT_read_opts(), TTget_recv(), TTRR_av_CB(), TTRR_load_CB(), TTRR_load_file(), TTRR_save_CB(), UC_read_opts(), UNIQ_idcode_fill(), unusuality(), update_PCOR_references(), update_references(), update_voxel_corr(), upsample_1(), upsample_1by2(), upsample_1by3(), upsample_1by4(), upsample_7(), vector_multiply(), vector_write(), VL_command_line(), VL_syntax(), warp3D_sharm2(), warp3D_sharm2_grad(), warp3D_sharm3(), warp3D_sharm3_grad(), winsor21_box_func(), winsor9_box_func(), write_images(), XSAVE_input(), XSAVE_output(), xvbcopy(), xxMRI_rotfunc(), xxMRI_scaler(), xxx_get_colormap(), xyz_to_ijk(), ZCAT_read_opts(), zedit_mask(), zero_bitvector(), zero_bitvector_piece(), zzmpco_(), zzmpli_(), and zzpsop_().

else shft = -1
 

Definition at line 87 of file AFNI_CoordChange.m.

Referenced by SUMA_OpenDX_Read(), SUMA_Reposition_Touchup(), SUMA_Suggest_Touchup(), and SUMA_Suggest_Touchup_Grad().

like RAI or [1 3 4] Mtrans is Morig in the new coordinate system Key Terms
 

Definition at line 1 of file AFNI_CoordChange.m.

like RAI or [1 3 4] Trans
 

Definition at line 1 of file AFNI_CoordChange.m.

end else TrCode = AFNI_OrientCode (Trans) Trans
 

Definition at line 74 of file AFNI_CoordChange.m.

 
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