Doxygen Source Code Documentation

AFNI_Index2XYZcontinuous.m File Reference


Functions
	if (nargin==3) if(~isempty(CoordCode))
make sure Indx is the right size switch	size (Indx, 2)
The equations that would change the indices to coordinate system result in a coordinate system that may be any permutation of	RAI (like IRA or AIR or IAR or RIA or ARI) so one only needs to find the%dimension permutation needed to bring the final result to RAI.%determine the ordering map to go from any permutation of RAI to RAI%[maploc(1)
	XYZmm (:, maploc(2))
	XYZmm (:, maploc(3))
	XYZmm (:, 2)
	XYZmm (:, 3)
back to the original	XYZmm (:, 1)
Now this is in the axis orientation which is Info	Orientation (:, 1)'called 3dmm in thd_coords.c[err
	if (ChangeCoord)
Variables
	function [err, XYZdic]
the default is RAI The code can be either a string or a vector of numbers(see AFNI_CoordChange for more on that)%%Output Parameters Debug Flag	DBG = 1
	ChangeCoord = 0
end end initailize return variables	err = 1
	XYZmm = []
make sure Indx is the right size switch	case = find(B_Info.Orientation == 'I')
make sure Indx is the right size switch change D index to XYZ	index [err, Indx]
make sure Indx is the right size switch change D index to XYZ OK	otherwise
The equations that would change the indices to coordinate system result in a coordinate system that may be any permutation of	jnk = find(Info.Orientation == 'R')
	Feb
Now this is in the axis orientation which is Info	XYZdic
Now this is in the axis orientation which is Info	map = THD_3dmm_to_dicomm (Info, XYZmm)
	return

Function Documentation

(

ChangeCoord

)

if ( nargin = = 3 )

Now this is in the axis orientation which is Info Orientation	(	:	,
		1
	)

The equations that would change the indices to coordinate system result in a coordinate system that may be any permutation of RAI

(

like IRA or AIR or IAR or RIA or

ARI

)

make sure Indx is the right size switch size	(	Indx	,
		2
	)

Referenced by AFNI_make_ptmask(), AFNI_make_tagmask(), AFNI_make_warp(), AFNI_marks_quality_check(), allocate_colors(), arg_verify(), assign_min_max(), calc_hist(), calc_stats(), calloc(), check_for_valid_inputs(), colormap_stream(), commlen(), copy_data(), countBytes(), create_image_data(), DCM_GetCompressedValue(), DCM_OpenFile(), DCM_ReadStream(), do_ncdump(), do_stats(), docommon(), EDIT_cluster_array(), emit_bits(), fail_die_malloc(), fail_die_malloc_die(), fail_die_realloc(), file_block_putter(), float_list_alloc(), get_chroma_dc_dct_diff(), get_luma_dc_dct_diff(), get_mask_size(), Gif_Unoptimize(), glutSolidCube(), glutWireCube(), grabPixels(), identify_clusters(), init_MCW_sizes(), initialize(), InitRLE(), iochan_init(), iochan_recv(), iochan_send(), JMovie2JPEG(), l_CHAR(), linear_reg(), LoadRLEVoxels(), main(), malloc(), mean_array(), MemAlloc(), mpeg2_convert(), mpeg2_header_picture(), mpeg2_malloc(), my_alloc(), my_fgets(), My_Malloc(), nc_def_dim(), new_NC_dim(), num_places(), p1gets(), Page_AllowAccess(), Page_Create(), Page_Delete(), Page_DenyAccess(), pm_allocarray(), pm_allocrow(), printNumber(), prolog(), pwritf_(), qh_copypoints(), qh_degen_redundant_neighbors(), qh_find_newvertex(), qh_findbestneighbor(), qh_gethash(), qh_joggleinput(), qh_markkeep(), qh_memalloc(), qh_memfree(), qh_memsize(), qh_merge_degenredundant(), qh_newhashtable(), qh_nextfurthest(), qh_partitionall(), qh_partitionvisible(), qh_point_add(), qh_printsummary(), qh_projectinput(), qh_setappend_set(), qh_setcheck(), qh_setcompact(), qh_setcopy(), qh_setduplicate(), qh_setfree(), qh_setfreelong(), qh_setindex(), qh_setlarger(), qh_setlast(), qh_setnew(), qh_setnew_delnthsorted(), qh_setprint(), qh_setsize(), qh_settruncate(), qh_setzero(), qh_updatetested(), qh_vertexridges(), qh_voronoi_center(), r_any_cb_fill_stats(), r_get_max_u_short(), r_histogram(), r_sprintf_long_to_hex(), read_color_table(), read_iqm(), read_piece(), readData(), readFile(), readFile1(), readGroupElement(), readPreamble(), readSequence(), readVRLength(), realloc(), sample1(), sample2(), scanCompressedPixels(), seek_chunk(), setBufferSize(), SetGOPSize(), setup_other_props(), shm_create(), SHM_create(), sort_permutation(), StoreRLEVoxels(), StoreTable(), suboffset(), SUMA_Addto_ROIplane_List(), SUMA_AssembleAllROIList(), SUMA_AssembleColorPlaneList(), SUMA_AssembleGroupList(), SUMA_calloc_fn(), SUMA_DrawLineAxis(), SUMA_grabPixels(), SUMA_malloc_fn(), SUMA_realloc_fn(), SwapOctreeNode(), SwapVoxels(), SwapWords(), T3D_geometry_parent_CB(), T3D_origin_av_CB(), T3D_read_images(), T3D_set_dependent_geometries(), T3D_size_av_CB(), testdims(), thd_mask_from_brick(), unoptimize_image(), valloc(), VPCheckClassifier(), VPCheckRawVolume(), VPCheckVoxelFields(), vpLoadClassifiedVolume(), vpLoadMinMaxOctree(), vpLoadRawVolume(), vpStoreClassifiedVolume(), vpStoreMinMaxOctree(), vpStoreRawVolume(), wr_ardecls(), wr_array_init(), wr_one_init(), write_char_init(), write_image(), WRite_iqm(), write_logical_screen_descriptor(), write_piece(), x_rsne(), x_wsne(), and XcgLiteClueAddWidget().

back to the original XYZmm	(	:	,
		1
	)

XYZmm	(	:	,
		3
	)

XYZmm	(	:	,
		2
	)

XYZmm	(	:	,
		maploc(3)
	)

XYZmm	(	:	,
		maploc(2)
	)

Variable Documentation

end case = find(B_Info.Orientation == 'I')

Definition at line 739 of file SumsOfSquares.m.

ChangeCoord = 0

Definition at line 50 of file AFNI_Index2XYZcontinuous.m.

the default is RAI The code can be either a string or a vector of numbers (see AFNI_CoordChange for more on that) % %Output Parameters Debug Flag DBG = 1

Definition at line 45 of file AFNI_Index2XYZcontinuous.m.

end err = 1

Definition at line 101 of file AFNI_Index2XYZcontinuous.m.

Feb

Definition at line 90 of file AFNI_Index2XYZcontinuous.m.

function[err, XYZdic]

Initial value:

 AFNI_Index2XYZcontinuous (Indx, Info, CoordCode)
%
%   [err,XYZdic] = AFNI_Index2XYZcontinuous (Indx, Info, [CoordCode])
%
%Purpose:
%   Change from voxel XYZindex (called Voxel Coords in AFNI) to XYZ in mm 
%   The mm and voxel coordinates refer to the values displayed 
%   on the top left corner of AFNI controller.
%   CoordCode is the one you'd set from the Coord Order plugin
%   
%   
%Input Parameters:
%   Indx an Mx3 matrix or an  Mx1 vector containing the voxel indices to be
%        transformed to voxel coordinates.  (indices start at 0)
%   Info is the output of BrikInfo
%   CoordCode is an optional parameter used to specify the coordinates system of the output
%      if empty or not specified

Definition at line 1 of file AFNI_Index2XYZcontinuous.m.

make sure Indx is the right size switch change D index to XYZ index[err, Indx]

Initial value:

 AfniIndex2AfniXYZ (Indx, Info.DATASET_DIMENSIONS(1), Info.DATASET_DIMENSIONS(2))
        case 3

Definition at line 62 of file AFNI_Index2XYZcontinuous.m.

The equations that would change the indices to coordinate system result in a coordinate system that may be any permutation of jnk = find(Info.Orientation == 'R')

Definition at line 76 of file AFNI_Index2XYZcontinuous.m.

Referenced by main(), SUMA_EquateSurfaceSize(), SUMA_getoffsets(), SUMA_ProjectSurfaceToSphere(), SUMA_readFScurv(), and SUMA_SureFit_Read_Topo().