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GE_createSPMmat.m File Reference

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Functions
	M (1:3, 1:3)
	M (1:3, 4)
Variables
Write SPM mat file function	M
Compute the coordinate system in the image plane	tlhc = [ im_hdr.tlhc_R
im_hdr	tlhc_A
im_hdr	tlhc_S
Top Left Hand Corner of Image	trhc = [ im_hdr.trhc_R
im_hdr	trhc_A
im_hdr	trhc_S
Top Right Hand Corner of Image	brhc = [ im_hdr.brhc_R
im_hdr	brhc_A
im_hdr	brhc_S
Bottom Right Hand Corner of Image	x = trhc - tlhc
xhat	y = trhc - brhc
yhat The normal to the plane	norm = [ im_hdr.norm_R
im_hdr	norm_A
im_hdr	norm_S
The directional normal	z = scandir * norm
zhat Build the M matrix for SPM M takes a voxel from the image and gives it a coordinate in mm On the scanner the voxels start in the top left hand corner of the first image In SPM they start in the bottom left hand	corner
zhat Build the M matrix for SPM M takes a voxel from the image and gives it a coordinate in mm On the scanner the voxels start in the top left hand corner of the first image In SPM they start in the bottom left hand so flip y and set the origin to tlhc	NB
zhat Build the M matrix for SPM M takes a voxel from the image and gives it a coordinate in mm On the scanner the voxels start in the top left hand corner of the first image In SPM they start in the bottom left hand so flip y and set the origin to tlhc should have position tlhc	Rot = [x, -y, z]

Function Documentation

M	(	1:3	,
		4
	)

M	(	1:3	,
		1:3
	)

Variable Documentation

Top Right Hand Corner of Image brhc = [ im_hdr.brhc_R

Definition at line 25 of file GE_createSPMmat.m.

Definition at line 25 of file GE_createSPMmat.m.

Definition at line 25 of file GE_createSPMmat.m.

zhat Build the M matrix for SPM M takes a voxel from the image and gives it a coordinate in mm On the scanner the voxels start in the top left hand corner of the first image In SPM they start in the bottom left hand corner

Definition at line 38 of file GE_createSPMmat.m.

Referenced by AFNI_init_warp(), and warp_corners().

M

Initial value:

 GE_createSPMmat(im_hdr, scandir)
%
% Put the appropriate translations and rotations to the M matrix
% given the information in the image header and the direction of
% acquisition
%
% S. Inati
% Dartmouth College
% Apr. 2001
%

% The conversion from pixels to mm
Dims = diag( [im_hdr.pixsize_X, ...
              im_hdr.pixsize_Y, ...
              im_hdr.slthick + im_hdr.scanspacing ])

Definition at line 42 of file GE_createSPMmat.m.

zhat Build the M matrix for SPM M takes a voxel from the image and gives it a coordinate in mm On the scanner the voxels start in the top left hand corner of the first image In SPM they start in the bottom left hand so flip y and set the origin to tlhc NB

Definition at line 38 of file GE_createSPMmat.m.

yhat The normal to the plane norm = [ im_hdr.norm_R

Definition at line 31 of file GE_createSPMmat.m.

Referenced by bandv_(), cinvit_(), comlr2_(), comqr2_(), comqr_(), hqr2_(), hqr_(), invit_(), norm2seg_angle(), qh_gram_schmidt(), qh_normalize2(), SUMA_OrientTriangles(), SUMA_Reposition_Touchup(), SUMA_StretchToFitLeCerveau(), SUMA_Suggest_Touchup(), SUMA_Suggest_Touchup_Grad(), SUMA_TriNorm(), tinvit_(), tsturm_(), and vpScanlineNormals().

Definition at line 31 of file GE_createSPMmat.m.

Definition at line 31 of file GE_createSPMmat.m.

zhat Build the M matrix for SPM M takes a voxel from the image and gives it a coordinate in mm On the scanner the voxels start in the top left hand corner of the first image In SPM they start in the bottom left hand so flip y and set the origin to tlhc should have position tlhc Rot = [x, -y, z]

Definition at line 41 of file GE_createSPMmat.m.

Compute the coordinate system in the image plane tlhc = [ im_hdr.tlhc_R

Definition at line 23 of file GE_createSPMmat.m.

Definition at line 23 of file GE_createSPMmat.m.

Definition at line 23 of file GE_createSPMmat.m.

Top Left Hand Corner of Image trhc = [ im_hdr.trhc_R

Definition at line 24 of file GE_createSPMmat.m.

Definition at line 24 of file GE_createSPMmat.m.

Definition at line 24 of file GE_createSPMmat.m.

x = trhc - tlhc

Referenced by __glutCreateWindow(), __glutFinishMenu(), __glutStartMenu(), AddBMotionBlock(), AddMotionBlock(), afi2o(), AFNI_brick_to_mri(), AFNI_drive_addto_graph_xy(), AFNI_faceup(), AFNI_find_closest_node(), AFNI_get_xhair_node(), AFNI_splashup(), afo2i(), AGNI_nod_to_NIML_row(), AGNI_nod_to_NIML_rows(), algdiv(), alngam(), alnrel(), apply_fill_radius(), apply_frame(), apply_image(), apply_image_disposal(), apser(), argmax_(), argnum_(), B64_to_base64(), B64_to_binary(), basis_cos(), basis_evaluation(), basis_expr(), basis_gam(), basis_legendre(), basis_sin(), basis_spmg1(), basis_spmg2(), basis_tent(), bcorr(), bell2_(), beta_p2t(), beta_t2p(), betadf(), bfrac(), bgrat(), BlockComputeSNR(), BlockifyFrame(), BlockToData(), bool_(), bpser(), bratio(), brcmp1(), brcomp(), bsort_(), build_ycc_rgb_table(), bup(), BYTE_VEC(), byteswap4(), byteswap8(), c_conj(), c_get(), c_mult(), c_padd(), c_scale(), calc_CC(), calc_linear_regression(), calc_matrices(), calc_reduced_model(), calc_resids(), calc_response(), calc_sse(), calc_sse_fit(), CalcDistortion(), calculate_min_code_bits(), calculate_ss(), calculate_y(), cdfbet(), cdfchi(), cdfchn(), cdfgam(), cdfnor(), check_norm_dirs(), chisq_p2t(), chisq_t2p(), cinvit_(), cl1_fort(), cl1_solve(), cl1_solve_res(), colormap_image_floyd_steinberg(), colormap_stream(), ComputeBlockColorDiff(), ComputeBMotionBlock(), ComputeBMotionLumBlock(), ComputeDiffDCTBlock(), ComputeHalfPixelData(), ComputeOctreeMask(), conspower(), coord_decode(), corcol(), correlate(), correlate_prep(), Cpointer(), Cpointer_PIXWIN(), create_row(), CreateGraphWindow(), CreateMainWindow(), CreatePyramid(), crop_image(), cumbet(), cumchi(), cumchn(), cumgam(), cumnor(), curve_(), d_abs(), d_acos(), d_asin(), d_atan(), d_atn2(), d_cos(), d_cosh(), d_exp(), d_int(), d_lg10(), d_log(), d_mod(), d_nint(), d_sign(), d_sin(), d_sinh(), d_sqrt(), d_tan(), d_tanh(), dbesj0_(), dbesj1_(), dbesy0_(), dbesy1_(), dct8_ref(), derf_(), derfc_(), DescendPyramid(), determineMBCount(), detrend(), devlpl(), dexpm1(), dinvr(), discard(), discard_Key(), dlanor(), dln1mx(), dln1px(), DoBIntraCode(), DoIntraCode(), draw_image_line(), draw_xhairs_in_image(), drawGraf(), DrawSubWindow(), dsort(), dt1(), dtos(), dtree_delete_coords(), dzror(), E0000(), E0001(), e_d(), elmbak_(), elmhes_(), EncodeScanline(), epslon_(), erf1(), erf_(), erfc1(), erfc_(), estimate(), esum(), EvalSpline(), expand_difference_bounds(), ExtractRawVolume(), f__canseek(), f__isdev(), f__nowreading(), f__nowwriting(), f_back(), f_inqu(), f_mult(), f_open(), FactorAffineView(), FactorPerspectiveView(), fd_txt(), ff_(), fft(), fill_area(), fill_data_area(), FIM_selection(), find_difference_bounds(), find_nearby_colors(), flconst(), flip_image(), float_to_complex(), fpser(), FramesToMPEG(), from_3dmm(), frstpt_(), Fsize_Validate(), g_char(), gaminv(), gamln1(), gamma_p2t(), gamma_t2p(), gaudf(), GenBFrame(), GenerateGrafFunc(), GenIFrame(), GenPFrame(), get_fft_mag(), get_popup_label(), get_siemens_extra_info(), get_used_colors(), Get_X_Y(), getnum(), Gif_AddComment(), Gif_AddCommentTake(), Gif_Debug(), glt_analysis(), glutCreateSubWindow(), glutGet(), glutInit(), glutInitWindowPosition(), glutPositionWindow(), GOPStoMPEG(), GRAF_drawing_EV(), GRAF_handle_CB(), grat1(), gratio(), gsumln(), h_abs(), h_dnnt(), h_nint(), h_sign(), hanning(), hash(), HI_keep(), hilbertdelay_V2(), histogram(), hmode_(), hookup(), hqr2_(), hqr_(), i_abs(), i_dnnt(), i_nint(), i_sign(), ibeta(), idct8_ref(), ifft(), ijk_invwarp(), ijkwarp(), incbeta(), init_indep_var_matrix(), InitSpline(), invit_(), ISQ_drawing_EV(), l_write(), Lagrange_interp(), land_(), lbit_bits(), lbit_cshift(), legendre(), legendre_(), linear_filter_extend(), linear_filter_trend(), linear_filter_zero(), linear_interp(), linear_reg(), list_decls(), lmode_(), lmofn_(), Load_Any_Arr(), Load_Any_ind(), Load_Any_RGB(), Load_Next_Arr(), Load_Next_ind(), Load_Next_RGB(), load_rect_str(), log10qg(), lor_(), LumBlockMAD(), LumMotionError(), mad_(), main(), make_belt(), make_plot(), mapMenu(), matrix_sqrt(), max_float(), MD5Transform(), mean_(), median_(), merge_cohar(), merge_colormap_if_possible(), min_float(), minfit_(), mk_hashtab(), mkbitcon(), mp_quant_zig_block(), mri_3dalign_edging(), mri_drawemptyrectangle(), mri_drawfilledrectangle(), mri_drawtext(), mypow(), mytanh(), ne_d(), NI_stream_readbuf64(), NI_write_columns(), NIML_to_AGNI_nod(), normal(), normal_p2t(), normal_t2p(), orstat_(), orthogonalise(), overlay_txt(), p10(), padd(), paintSubMenuArrow(), pareval_(), parevec_(), parse_rectangle(), PERMTEST_compute(), picture_display_ext(), plot_fdX(), plot_graphs(), plot_image_surface(), plot_line(), PLOT_scatterellipse(), plot_ts_addto(), plot_ts_lab(), plot_ts_mem(), plot_ts_qqq(), plotpak_curve(), plotpak_frstpt(), plotpak_points(), plotpak_pwrit(), plotpak_pwritf(), plotpak_srface(), plotpak_vector(), plotx(), PLUTO_scatterplot(), plx_TXT(), plx_txt(), pmodel_cdf(), pmodel_pdf(), pnm_blackxel(), pnm_whitexel(), PNMtoYUV(), point_(), points_(), poly_field(), pow_di(), pow_hh(), pow_ii(), pow_qq(), pow_ri(), pow_zi(), pow_zz(), ppmd_circle(), ppmd_filledrectangle(), ppmd_polyspline(), ppmd_text(), PPMtoYUV(), prconr(), print_plot(), process(), ps_arc(), ps_circle(), psi(), PSubSampleSearch(), put_background_in_screen(), put_image_in_screen(), pwrit_(), pwritf_(), qbit_bits(), qbit_cshift(), qg(), qg_(), quadrant_corr(), quadrant_manycorr(), qzvec_(), r_abs(), r_acos(), r_asin(), r_atan(), r_atn2(), r_cos(), r_cosh(), r_exp(), r_int(), r_lg10(), r_log(), r_mod(), r_nint(), r_sign(), r_sin(), r_sinh(), r_sqrt(), r_tan(), r_tanh(), rcomp(), RCREND_cutout_set_CB(), rd_F(), rd_I(), rd_Z(), Read_file(), Read_part_file_delay(), read_test(), ReadAYUV(), ReadPNM(), ReadSub4(), rebak_(), rebakb_(), rect_(), recurseSelect(), redraw_graph(), redraw_MCW_pasgraf(), reduc2_(), reduc_(), remove_field(), REND_cutout_set_CB(), RepackClassifiedVolume(), rexp(), rfft(), rlog(), rlog1(), rotate_image(), RWC_drag_circle(), RWC_drag_rectangle(), save_act_im(), save_all_images(), save_avr_array(), sem_(), Setup_keys(), ShowBBMVHistogram(), ShowBFMVHistogram(), ShowPMVHistogram(), sign(), signal_model(), simple_frame_data(), Smooth_line(), spearman_rank_corr(), spearman_rank_manycorr(), srface_(), stas4(), stdev_(), step_(), stree_extract_max(), stree_insert(), subW_TXT(), sum32(), SUMA_add_node_ixyz(), SUMA_addNode(), SUMA_AddToBrushStroke(), SUMA_Apply_VolReg_Trans(), SUMA_BinaryZeroSearch(), SUMA_Find_inIntVect(), SUMA_FromToRotation(), SUMA_GetSelectionLine(), SUMA_isSkin(), SUMA_Ply_Read(), SUMA_Read_2Ddfile(), SUMA_Read_2Dfile(), SUMA_Read_dfile(), SUMA_Read_file(), SUMA_UniqueInt(), SUMA_z_doubqsort(), SUMA_z_dqsort(), SUMA_z_dqsort_nsc(), SUMA_z_qsort(), svd_(), take_file_name(), tb_project_to_sphere(), tent_(), THD_3mni_to_3tta(), THD_3tta_to_3mni(), THD_pearson_corr(), THD_quadrant_corr(), THD_spearman_corr(), THRESH_compute(), THRESH_mask_brain(), THRESH_region_grow(), tnonc_s2p(), to_3dmm(), Track_Cursor(), Track_Vpointer(), transp_frame_data(), TransposeBlock(), trn32s_(), uran_(), vector_(), vpBicubicFilter(), VPClassifyBlock(), VPComputeWarpTables(), vpGaussianFilter(), vpGetImage(), vpLinearFilter(), vpNormalIndex(), Vpointer(), VPQuantize(), vpRamp(), vpScanlineNormals(), VPShadeBlock(), VPWarpA101N(), VPWarpA110N(), VPWarpA111N(), VPWarpA301N(), VPWarpA330N(), VPWarpA330R(), VPWarpA331N(), VPWarpA331R(), vset(), w3dMRI_affine(), w3dMRI_scaler(), warp3D_sharm2(), warp3D_sharm2_grad(), warp3D_sharm3(), warp3D_sharm3_grad(), warp_image(), weighted_index(), WORD_VEC(), wr_globals(), wr_one_init(), write_float(), wrt_F(), wrt_G(), wrt_I(), wrt_IM(), wrt_L(), Xgamm(), xyz_to_ijk(), zeromean(), ZeroMotionSufficient(), ztone(), ztone_(), zzaxyy_(), zzliny_(), zzlogy_(), and zzphys_().

return end Write the data switch Opt case y = trhc - brhc

Definition at line 106 of file wryte3.m.

Referenced by __glutCreateWindow(), __glutFinishMenu(), __glutPaintMenu(), __glutStartMenu(), AddBMotionBlock(), AddMotionBlock(), afi2o(), AFNI_brick_to_mri(), AFNI_drive_addto_graph_1D(), AFNI_drive_addto_graph_xy(), AFNI_faceup(), AFNI_find_closest_node(), AFNI_get_xhair_node(), AFNI_splashup(), afo2i(), AGNI_nod_to_NIML_row(), AGNI_nod_to_NIML_rows(), apply_fill_radius(), apply_frame(), apply_image(), apply_image_disposal(), B64_to_base64(), B64_to_binary(), beta_p2t(), beta_t2p(), bfrac(), bgrat(), BlockComputeSNR(), BlockifyFrame(), BlockToData(), bratio(), brcmp1(), brcomp(), bup(), c_conj(), c_get(), c_mult(), c_padd(), c_scale(), calc_CC(), calc_coef(), calc_linear_regression(), calc_reduced_model(), calc_resids(), calc_sse(), calc_sse_fit(), calc_sspe(), CalcDistortion(), calculate_min_code_bits(), calculate_results(), calculate_ssa(), calculate_ssab(), calculate_ssabc(), calculate_ssac(), calculate_ssb(), calculate_ssbc(), calculate_ssbca(), calculate_ssc(), calculate_ssca(), calculate_sse(), calculate_ssijkm(), calculate_ssto(), calculate_sstr(), calculate_sum(), calculate_y(), calculate_ysum(), cdfbet(), check_norm_dirs(), cinvit_(), cl1_solve(), cl1_solve_res(), ComputeBlockColorDiff(), ComputeBMotionBlock(), ComputeBMotionLumBlock(), ComputeDiffDCTBlock(), ComputeHalfPixelData(), ComputeMotionBlock(), ComputeMotionLumBlock(), ComputeOctreeMask(), coord_decode(), copy_data_area(), correlate(), correlate_prep(), Cpointer(), Cpointer_PIXWIN(), create_row(), CreateGraphWindow(), CreateMainWindow(), CreatePyramid(), crop_image(), cubic_spline(), cumbet(), cumnor(), curve_(), d_atn2(), d_mod(), DescendPyramid(), determineMBCount(), detrend(), do_xrestore_stuff(), DoBIntraCode(), DoIntraCode(), draw_image_line(), drawGraf(), DrawSubWindow(), dtree_delete_coords(), elmhes_(), EncodeScanline(), expand_difference_bounds(), ExtractRawVolume(), f_back(), f_mult(), FactorAffineView(), FactorPerspectiveView(), fd_txt(), fill_area(), fill_data_area(), FIM_selection(), find_difference_bounds(), flip_image(), Frame_AllocDecoded(), Frame_AllocHalf(), Frame_AllocPPM(), Frame_AllocYCC(), FramesToMPEG(), from_3dmm(), frstpt_(), Fsize_Validate(), g_char(), gaminv(), GenBFrame(), GenerateGrafFunc(), GenIFrame(), GenPFrame(), get_fft_mag(), get_popup_label(), get_siemens_extra_info(), get_used_colors(), Get_X_Y(), GetRemoteDecodedRefFrame(), GetRemoteFrame(), Gif_ClipImage(), glt_analysis(), glutCreateSubWindow(), glutGet(), glutInit(), glutInitWindowPosition(), glutPositionWindow(), GOPStoMPEG(), GRAF_drawing_EV(), GRAF_handle_CB(), gratio(), h2v1_merged_upsample(), h2v2_merged_upsample(), hilbertdelay_V2(), histogram(), hookup(), hqr2_(), hqr_(), ijk_invwarp(), ijkwarp(), incbeta_inverse(), InitNormalTables(), InitSpline(), invit_(), ISQ_drawing_EV(), l_write(), Lagrange_interp(), lbit_bits(), lbit_cshift(), linear_interp(), linear_reg(), Load_Any_Arr(), Load_Any_ind(), Load_Any_RGB(), Load_Next_Arr(), Load_Next_ind(), Load_Next_RGB(), load_rect_str(), LumAddMotionError(), LumBlockMAD(), LumMotionError(), main(), make_belt(), make_plot(), mapMenu(), merge_cohar(), minfit_(), mk_hashtab(), mkbitcon(), mp_fwd_dct_fast(), mp_quant_zig_block(), mri_3dalign_edging(), mri_drawemptyrectangle(), mri_drawfilledrectangle(), mri_drawtext(), mypow(), namelist(), NI_stream_readbuf64(), NI_write_columns(), NIML_to_AGNI_nod(), orthogonalise(), overlay_txt(), p10(), padd(), paintMenuItem(), paintSubMenuArrow(), pareval_(), parevec_(), parse_rectangle(), PERMTEST_compute(), picture_display_ext(), plot_fdX(), plot_graphs(), plot_image_surface(), plot_line(), PLOT_scatterellipse(), plot_strip_addto(), plot_ts_addto(), plot_ts_lab(), plot_ts_mem(), plot_ts_qqq(), PLOT_tsgray(), plotpak_curve(), plotpak_frstpt(), plotpak_points(), plotpak_pwrit(), plotpak_pwritf(), plotpak_srface(), plotpak_vector(), plotx(), PLUTO_scatterplot(), plx_TXT(), plx_txt(), PNMtoYUV(), point_(), points_(), poly_field(), pow_zz(), ppmd_circle(), ppmd_filledrectangle(), ppmd_polyspline(), ppmd_text(), PPMtoYUV(), print_plot(), ps_arc(), ps_circle(), put_background_in_screen(), put_image_in_screen(), pwrit_(), pwritf_(), qbit_bits(), qbit_cshift(), qzvec_(), r_atn2(), r_mod(), RCREND_cutout_set_CB(), read_test(), ReadAYUV(), ReadDecodedRefFrame(), ReadEYUV(), ReadPNM(), ReadPPM(), ReadSub4(), ReadY(), recurseSelect(), redraw_graph(), reduc2_(), reduc_(), regression_analysis(), REND_cutout_set_CB(), RepackClassifiedVolume(), Resize_Height(), Resize_Width(), rfft(), rotate_image(), RWC_drag_circle(), RWC_drag_rectangle(), save_act_im(), save_all_images(), save_avr_array(), save_voxel(), SendDecodedFrame(), Setup_keys(), ShowBBMVHistogram(), ShowBFMVHistogram(), ShowPMVHistogram(), simple_frame_data(), Smooth_line(), srface_(), StartIOServer(), STATS_tsfunc(), stree_extract_max(), stree_insert(), stvaln(), subW_TXT(), SUMA_add_node_ixyz(), SUMA_addNode(), SUMA_AddToBrushStroke(), SUMA_Apply_VolReg_Trans(), SUMA_GetSelectionLine(), SUMA_isSkin(), SUMA_Ply_Read(), SUMA_reorder(), SUMA_UniqueInt(), svd_(), T3D_check_outliers(), take_file_name(), tb_project_to_sphere(), THD_3mni_to_3tta(), THD_3tta_to_3mni(), THD_pearson_corr(), THD_quadrant_corr(), THD_spearman_corr(), THRESH_compute(), THRESH_mask_brain(), THRESH_region_grow(), tnonc_s2p(), to_3dmm(), Track_Cursor(), Track_Vpointer(), transp_frame_data(), TransposeBlock(), trn32s_(), vector_(), VPAffineImageOverlap(), VPClassifyBlock(), vpClassifyScalars(), vpClassifyVolume(), VPComputeWarpTables(), vpGetImage(), vpNormalIndex(), Vpointer(), VPQuantize(), vpRamp(), VPShadeBlock(), vpVolumeNormals(), VPWarpA101N(), VPWarpA110N(), VPWarpA111N(), VPWarpA301N(), VPWarpA330N(), VPWarpA330R(), VPWarpA331N(), VPWarpA331R(), vset(), w3dMRI_affine(), w3dMRI_scaler(), warp3D_sharm2(), warp3D_sharm2_grad(), warp3D_sharm3(), warp3D_sharm3_grad(), weighted_index(), wr_globals(), write_image_data(), WriteDecodedFrame(), xyz_to_ijk(), ycc_rgb_convert(), ycck_cmyk_convert(), zeromean(), ZeroMotionSufficient(), ztone(), ztone_(), zzaxxx_(), zzlinx_(), zzlogx_(), and zzphys_().

The directional normal z = scandir * norm

Definition at line 33 of file GE_createSPMmat.m.

Referenced by afi2o(), AFNI_brick_to_mri(), AFNI_find_closest_node(), AFNI_get_xhair_node(), afo2i(), AGNI_nod_to_NIML_row(), AGNI_nod_to_NIML_rows(), apply_fill_radius(), B64_to_base64(), B64_to_binary(), basym(), betaln(), bgrat(), bpser(), bratio(), brcmp1(), brcomp(), c_abs(), c_cos(), c_exp(), c_log(), c_mult(), c_sin(), c_sqrt(), calculate_results(), cdfnor(), cds(), check_norm_dirs(), cl1_solve(), cl1_solve_res(), ComputeOctreeMask(), coord_decode(), create_row(), CreatePyramid(), d_cnjg(), d_imag(), d_mod(), DescendPyramid(), dlnbet(), dsort(), dstrem(), dtree_delete_coords(), EncodeScanline(), estimate(), ExtractRawVolume(), f_back(), f_mult(), FactorAffineView(), FactorPerspectiveView(), from_3dmm(), gaminv(), gaudf(), get_siemens_extra_info(), get_time(), grat1(), gratio(), ijk_invwarp(), ijkwarp(), initialize(), initialize_slice_sequence(), l_write(), lbit_cshift(), main(), make_plot(), mkbitcon(), mri_3dalign_edging(), NI_stream_readbuf64(), NI_write_columns(), NIML_to_AGNI_nod(), normal(), PERMTEST_compute(), pfit(), plot_image_surface(), plotpak_srface(), psi(), qbit_cshift(), r_cnjg(), r_imag(), r_mod(), RCREND_cutout_set_CB(), read_test(), recurseSelect(), REND_cutout_set_CB(), RepackClassifiedVolume(), segment_x_slices(), segment_y_slices(), segment_z_slices(), spmpar(), STATS_tsfunc(), stree_extract_max(), stree_insert(), stvaln(), SUMA_add_node_ixyz(), SUMA_addNode(), SUMA_Apply_VolReg_Trans(), SUMA_isSkin(), SUMA_Ply_Read(), tb_project_to_sphere(), THD_3mni_to_3tta(), THD_3tta_to_3mni(), THD_timeof(), THRESH_compute(), THRESH_mask_brain(), THRESH_region_grow(), threshold_data(), to_3dmm(), tqli(), TransposeBlock(), undoReversibleTransformation_fast(), undoReversibleTransformation_small(), volume_match(), VPClassifyBlock(), vpClassifyScalars(), vpClassifyVolume(), VPQuantize(), VPShadeBlock(), vpVolumeNormals(), vset(), w3dMRI_affine(), w3dMRI_scaler(), warp3D_sharm2(), warp3D_sharm2_grad(), warp3D_sharm3(), warp3D_sharm3_grad(), weighted_index(), wr_equiv_init(), Xgamm(), xyz_to_ijk(), z_abs(), z_cos(), z_exp(), z_log(), z_sin(), z_sqrt(), and ztone().

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