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DeOblique.m File Reference

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Functions

id Usage:say: (id filename,[say] may0603mj/I.610 DeOblique)
 while (~isempty(fname))
desired plane is one that
is parallel to Axial plane
and passing through ctr2 
switch (CardPlane(1))
id cnst ()
 fprintf (1,'Error Bad Plane.\n')

Variables

load image header RAS here
means LPI 
fname = sprintf('/home/ziad/tmp/pm040803/5to10/023/I.138')
get three points forming corners
of plane and the center of
the plane 
tlhc1 = GE_readHeader(fname) [im_hdr.tlhc_R im_hdr.tlhc_A im_hdr.tlhc_S]
 trhc1 = [im_hdr.trhc_R im_hdr.trhc_A im_hdr.trhc_S]
 brhc1 = [im_hdr.brhc_R im_hdr.brhc_A im_hdr.brhc_S]
 ctr1 = [im_hdr.ctr_R im_hdr.ctr_A im_hdr.ctr_S]
Tri1 XYZ = [tlhc1
an idea of the displacement
at the 
edges = Plane_Equation (Tri1)
an idea of the displacement
at the typically the minimum
of
d = 2 .* (tlhc1 - ctr1)
form the equation of the desired
plane 
ctr2 = ctr1
 CardPlane = sprintf('Axial')
desired plane is one that
is parallel to Axial plane
and passing through ctr2 case 
A
 Eq2 = [0 0 1 -ctr2(3)]
case C
case S
 otherwise
end find the intersection
line of the two planes 
u = cross(Eq1(1:3),Eq2(1:3))

Function Documentation

id cnst  )  [virtual]
 

fprintf ,
'Error Bad Plane.\n
 

desired plane is one that is parallel to Axial plane and passing through ctr2 switch CardPlane(1)   ) 
 

id Usage:say: id  filename,
[say] may0603mj/I.610  DeOblique
[virtual]
 

while isempty(fname)  ) 
 


Variable Documentation

desired plane is one that is parallel to Axial plane and passing through ctr2 case A
 

Definition at line 58 of file DeOblique.m.

brhc1 = [im_hdr.brhc_R im_hdr.brhc_A im_hdr.brhc_S]
 

Definition at line 43 of file DeOblique.m.

C
 

Initial value:

 DF C + DF AC
                
                 ssterm(6) = ssterm(6) + ssterm(7)

Referenced by SUMA_Convexity(), SUMA_Convexity_Engine(), SUMA_dPoint_At_Distance(), SUMA_Point_At_Distance(), and SUMA_SortedAxisSegmentList().

CardPlane = sprintf('Axial')
 

Definition at line 54 of file DeOblique.m.

ctr1 = [im_hdr.ctr_R im_hdr.ctr_A im_hdr.ctr_S]
 

Definition at line 42 of file DeOblique.m.

Referenced by SUMA_MapSurface().

form the equation of the desired plane ctr2 = ctr1
 

Definition at line 50 of file DeOblique.m.

Referenced by SUMA_MapSurface().

d = 2 .* (tlhc1 - ctr1)
 

Referenced by AFNI_find_closest_node(), algdiv(), allocate_closest(), analyze_results(), apply_image_disposal(), argsort(), bang(), basym(), bgrat(), bup(), byteswap4(), byteswap8(), c_bright(), c_squeeze(), calc_partial_derivatives(), calc_stat(), calculate_acontrasts(), calculate_adifferences(), calculate_ameans(), calculate_bcontrasts(), calculate_bdifferences(), calculate_bmeans(), calculate_sum(), calculate_xcontrasts(), calculate_xdifferences(), calculate_xmeans(), Clp_VaOptionError(), color_bright(), color_squeeze(), compare(), create_bucket(), cubic_spline(), cumnor(), def_start(), disp_f3_point(), disp_func_t(), disp_node_list_t(), disp_opts_t(), disp_param_t(), disp_parser_t(), disp_surf_t(), disp_v2s_plugin_opts(), disp_v2s_results(), dlngam(), dumpBinaryData(), E0001(), e_d(), fatali(), fill_area(), fold(), gam1(), gaminv(), gamln(), getdimen(), ind_printf(), initialize(), intersection_map(), list_print(), main(), make_plot(), MD5Transform(), median_float4(), mkrealcon(), normalize(), op_gen(), orient_side_rai(), other_undefs(), pentagon(), qSort3(), r_debug_check(), rd_disp_dset_info(), rd_disp_mri_image(), rd_disp_xhairs(), rd_F(), rd_set_debug_level(), rot_to_shear(), rot_to_shear_matvec(), simpleSort(), sin_func(), sin_grad(), SUMA_AdvancePastNumbers(), SUMA_BrushStrokeToNodeStroke(), SUMA_Convexity_Engine(), SUMA_dPoint_At_Distance(), SUMA_DrawAxis(), SUMA_EquateSurfaceAreas(), SUMA_EquateSurfaceVolumes(), SUMA_FromIntEdgeToIntEdge(), SUMA_GetNextCommand(), SUMA_Householder(), SUMA_isConsistent(), SUMA_isinbox(), SUMA_isNumString(), SUMA_MT_intersect_triangle(), SUMA_MT_isIntersect_Triangle(), SUMA_ok_orstring(), SUMA_Point_At_Distance(), SUMA_RegisterCommand(), SUMA_ReportDrawnROIDatumLength(), SUMA_SortedAxisSegmentList(), SUMA_StringToNum(), SUMA_SurfNorm(), SUMA_TriNorm(), tb_project_to_sphere(), terminate(), tqli(), trackball(), trackball_Phi(), tred2(), vector_multiply_subtract(), VPDumpClassifier(), vpResample(), wrt_E(), wrt_F(), wrt_G(), and Xgamm().

an idea of the displacement at the edges = Plane_Equation (Tri1)
 

Definition at line 44 of file DeOblique.m.

Referenced by nc_get_vara(), nc_get_vara_double(), nc_get_vara_float(), nc_get_vara_int(), nc_get_vara_long(), nc_get_vara_schar(), nc_get_vara_short(), nc_get_vara_text(), nc_get_vara_uchar(), nc_get_varm(), nc_get_varm_double(), nc_get_varm_float(), nc_get_varm_int(), nc_get_varm_long(), nc_get_varm_schar(), nc_get_varm_short(), nc_get_varm_text(), nc_get_varm_uchar(), nc_get_vars(), nc_get_vars_double(), nc_get_vars_float(), nc_get_vars_int(), nc_get_vars_long(), nc_get_vars_schar(), nc_get_vars_short(), nc_get_vars_text(), nc_get_vars_uchar(), nc_put_vara(), nc_put_vara_double(), nc_put_vara_float(), nc_put_vara_int(), nc_put_vara_long(), nc_put_vara_schar(), nc_put_vara_short(), nc_put_vara_text(), nc_put_vara_uchar(), nc_put_varm(), nc_put_varm_double(), nc_put_varm_float(), nc_put_varm_int(), nc_put_varm_long(), nc_put_varm_schar(), nc_put_varm_short(), nc_put_varm_text(), nc_put_varm_uchar(), nc_put_vars(), nc_put_vars_double(), nc_put_vars_float(), nc_put_vars_int(), nc_put_vars_long(), nc_put_vars_schar(), nc_put_vars_short(), nc_put_vars_text(), nc_put_vars_uchar(), NCedgeck(), NCiocount(), and SumaToGts().

Eq2 = [0 0 1 -ctr2(3)]
 

Definition at line 66 of file DeOblique.m.

V fname = sprintf('/home/ziad/tmp/pm040803/5to10/023/I.138')
 

Definition at line 84 of file GE_convertADW.m.

Referenced by add_to_flist(), AFNI_finalize_saveim_CB(), AFNI_finalize_write_palette_CB(), AFNI_find_jpegs(), AFNI_process_environ(), AFNI_process_setup(), AFNI_read_images(), AFNI_startup_layout_CB(), AFNI_startup_script_CB(), AFNI_suck_file(), backup(), bad_atypes(), check_dicom_magic_num(), COMPRESS_add_suffix(), COMPRESS_filecode(), COMPRESS_filename(), COMPRESS_fopen_read(), COMPRESS_fopen_write(), COMPRESS_has_suffix(), COMPRESS_unlink(), EDIT_dset_items(), extract_index(), extract_xyz(), get_argtypes(), get_dfile_params(), getenv_(), GIF_Read_File(), GRA_file_pixmap(), GRA_saver_CB(), IJKAR_reader(), imsized_fname(), is_file(), ISQ_saver_CB(), ISQ_snapfile(), JPEG_matrix_gray(), main(), MCW_file_expand(), MCW_filetype(), mcw_malloc_dump(), memplot_to_postscript(), mri_dicom_header(), mri_imcount(), mri_imcount_dicom(), mri_imcount_mpeg(), mri_possibly_dicom(), mri_read(), mri_read_1D(), mri_read_3A(), mri_read_3D(), mri_read_3D_delay(), mri_read_ascii(), mri_read_ascii_ragged(), mri_read_dicom(), mri_read_file(), mri_read_file_delay(), mri_read_just_one(), mri_read_mpeg(), mri_read_nsize(), mri_read_ppm(), mri_read_ppm3(), mri_read_ppm_header(), mri_read_stuff(), mri_write(), mri_write_1D(), mri_write_7D(), mri_write_analyze(), mri_write_angif(), mri_write_ascii(), mri_write_jpg(), mri_write_pnm(), mri_write_raw(), multivector_read(), multivector_write(), my_alloc(), NI_malloc_dump(), NI_read_file_nohead(), NI_read_URL_tmpdir(), NI_stream_open(), NLFIT_get_all_MODELs(), NLFIT_read_MODEL(), PBAR_read_bigmap(), Pfile(), PLUG_get_all_plugins(), PLUG_read_plugin(), proto(), ps_openpl(), psfinalize_CB(), qhull_wrap(), r_mri_read_dicom(), RCREND_finalize_saveim_CB(), RCREND_read_exec_CB(), RCREND_read_states(), RCREND_read_this_CB(), RCREND_save_many_CB(), RCREND_save_this_CB(), read_ascii_floats(), read_glt_matrix(), read_iqm(), read_URL_tmpdir(), REND_finalize_saveim_CB(), REND_read_exec_CB(), REND_read_states(), REND_read_this_CB(), REND_save_many_CB(), REND_save_this_CB(), RWC_read_time_series(), RWC_setup_fims(), save_argtypes(), saveargtypes(), select_file_name(), SER_new_vector(), SetupCollectQuantStats(), SetupWriteDistortions(), SFIM_load_intervals(), suck_file(), SUMA_AFNI_Extract_Colors(), SUMA_BinarySuck(), SUMA_BrainVoyager_Read_vmr(), SUMA_Cmap_To_SO(), SUMA_Cmap_To_SO_old(), SUMA_file_suck(), SUMA_LoadVisualState(), SUMA_OpenDX_Read(), SUMA_OpenDX_Read_CruiseVolHead(), SUMA_OpenDX_Read_SO(), SUMA_qhull_wrap(), SUMA_read_ppm(), SUMA_SaveVisualState(), SUMA_SphereQuality(), SUMA_StretchToFitLeCerveau(), SUMA_suck_file(), THD_fetch_1D(), THD_get_all_executables(), THD_get_all_timeseries(), THD_init_alldir_datablocks(), THD_init_prefix_datablocks(), THD_open_ctfmri(), THD_open_ctfsam(), THD_open_minc(), THD_open_one_dataset(), THD_read_dvecmat(), THD_trailname(), THD_write_1D(), THD_write_minc(), THD_write_nifti(), trailname(), TS_reader(), TTRR_load_file(), WRite_iqm(), XSAVE_input(), and XSAVE_output().

otherwise
 

Definition at line 67 of file DeOblique.m.

case S
 

Definition at line 64 of file DeOblique.m.

get three points forming corners of plane and the center of the plane tlhc1 = GE_readHeader(fname) [im_hdr.tlhc_R im_hdr.tlhc_A im_hdr.tlhc_S]
 

Definition at line 39 of file DeOblique.m.

trhc1 = [im_hdr.trhc_R im_hdr.trhc_A im_hdr.trhc_S]
 

Definition at line 43 of file DeOblique.m.

end find the intersection line of the two planes u = cross(Eq1(1:3),Eq2(1:3))
 

Definition at line 72 of file DeOblique.m.

Referenced by algdiv(), bandr_(), bandv_(), basym(), betaln(), bgrat(), bisect_(), bpser(), brcmp1(), brcomp(), bsGetUInt32(), bsPutUInt32(), cross_product(), dlnbet(), DMAT_svd(), dot_product(), fft(), gaminv(), gratio(), ifft(), InitSpline(), pow_di(), pow_hh(), pow_ii(), pow_qq(), pow_ri(), pow_zi(), ppmd_text(), pythag_(), rcomp(), rlog(), SUMA_FromToRotation(), SUMA_MT_isIntersect_Triangle(), SUMA_StretchToFitLeCerveau(), SUMA_Surf_Plane_Intersect(), SUMA_SurfGridIntersect(), svd_(), svd_double(), tinvit_(), tridib_(), and tsturm_().

Tri1 XYZ = [tlhc1
 

Definition at line 43 of file DeOblique.m.

 

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