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BrikLoad.m File Reference

Go to the source code of this file.


Functions

BrikName,[Opt] Purpose:Parameters: (id Input,[,] 2 DATASET_RANK)
Note that indexing in matlab
is different than in AFNI
Matlab starts indexing at
while AFNI starts with So 		voxel (i, j, k) in AFNI corresponds to voxel(i+1
plot the time course of voxel (29, 33, 3)%plot(squeeze(V(30
plot the time course of squeeze
is used to turn the x1x1x160
matrix into a x1 vector for
the plot function see also
WriteBrik The core for this 		function (fread and reshape) is based on%Timothy M.Ellmore's(Laboratory of Brain and Cognition
 if (~isstruct(param1))
 if (~isfield(Opt,'FileFormat'))
 if (isempty(Opt.FileFormat))
 if (~isempty(xtr))
end elseif (strcmp(Opt.FileFormat, '1D')|strcmp(Opt.FileFormat, '1d'))
end if (is1D)
 if (~isfield(Opt, 'method')|isempty(Opt.method))
end if (isfield(Opt,'Slices')&~isempty(Opt.Slices))
end if (length(Opt.Slices)~=1)
end if (~isfield(Opt, 'SliceSize_1D')|isempty(Opt.SliceSize_1D))
 if (isfield(Opt,'Frames')&~isempty(Opt.Frames))
 if (err)
end assume you have a brik
format and proceed as usual
make sure Opt fields are set
OK That s done for the new
usage format 		if (~isfield(Opt,'')|isempty(Opt.))
end if (~isfield(Opt,'Format')|isempty(Opt.Format))
end if (~isfield(Opt,'MachineFormat')|isempty(Opt.MachineFormat))
end if (~isfield(Opt,'Scale')|isempty(Opt.Scale))
end you can change the default
for the new usage here 		if (~isfield(Opt,'Slices')|isempty(Opt.Slices))
end if (~isfield(Opt,'Frames')|isempty(Opt.Frames))
end if (~isfield(Opt,'FileFormat')|isempty(Opt.FileFormat))
end set the format if (eq_str(Opt.Format,'vector'))
 elseif (eq_str(Opt.Format,'matrix'))
 if (~isempty(vtmp))
 if (~filexist(sHead))
end if (~filexist(sBRIK))
end get Brik info and setup
for slice and frame 		selectors (for FMRISTAT)[err
 if (~strcmp(Info.ByteOrder,'unspecified'))
found byte order make sure
it does not conflict with
the user option 		if (~isempty(Opt.MachineFormat))
found byte order make sure
it does not conflict with
the user option user specified
a format 		if (~strcmp(Info.ByteOrder, Opt.MachineFormat))
found byte order make sure
it does not conflict with
the user option user specified
a format warn 		ErrEval (FuncName,'Wrn_Machine format specified conflicts with.HEAD info.Proceeding with fread...')
end else did not find ByteOrder
in use user option or pick
default 		if (isempty(Opt.MachineFormat))
 ErrEval (FuncName,'Wrn_No Machine Format was specified by user or found in.HEAD file.Using ieee-be(MSB_FIRST)')
 if (length(itype) > 1)
 errordlg (ErrMessage)
 if (fidBRIK< 0)
if isallslices fseek (fidBRIK, numpix *Info.DATASET_DIMENSIONS(3)*(frame-1)*Info.TypeBytes, 'bof')
 V (istrt:istp)
 fseek (fidBRIK, numpix *(slice-1+Info.DATASET_DIMENSIONS(3)*(frame-1))*Info.TypeBytes, 'bof')
end end end end fclose (fidBRIK)
scale if required if (Opt.Scale) = AFNI_OrientCode(NewCode)
 if (~isempty(iscl))
end end end if reshape V if (~DoVect)
 size (V) figure(1)
 subplot (2, 2, k)
 imagesc (V(:,:, Opt.Slices(i), Opt.Frames(j)))
 if (exist('spectral')) colormap(spectral)
 figure (2)
 imagesc (V(:,:, i, j))
 colormap (spectral)

Variables

 function [err, V, Info, ErrMessage]
see New Usage [err, V, Info, ErrMessage]
see New name of the brik form
see New name of the brik vector
or matrix this is 		optional
plot the time course of squeeze
is used to turn the x1x1x160
matrix into a x1 vector for
the plot function see also 		BrikInfo
plot the time course of squeeze
is used to turn the x1x1x160
matrix into a x1 vector for
the plot function see also 		Info_1D
plot the time course of squeeze
is used to turn the x1x1x160
matrix into a x1 vector for
the plot function see also
WriteBrik The core for this
NIMH function ReadBRIK Slices
and Frames options were added
by Dr Keith Worsley for FMRISTAT 		http
plot the time course of squeeze
is used to turn the x1x1x160
matrix into a x1 vector for
the plot function see also
WriteBrik The core for this
NIMH function ReadBRIK Slices
and Frames options were added
by Dr Keith Worsley for FMRISTAT
Marquette University Biophysics
Research 		institute
plot the time course of squeeze
is used to turn the x1x1x160
matrix into a x1 vector for
the plot function see also
WriteBrik The core for this
NIMH function ReadBRIK Slices
and Frames options were added
by Dr Keith Worsley for FMRISTAT
Marquette University Biophysics
Research Medical College of
Wisconsin 		Contact
Debug Flag DBG = 1
initailize return variables err = 1
 V = []
 Info = []
 ErrMessage = ''
switch nargin
switch case
switch DoVect = 0
Opt MachineFormat = ''
Opt Format = 'matrix'
Opt Scale = 1
Opt Slices = []
Opt Frames = []
Opt FileFormat = ''
else Opt = param1
 otherwise
 return
end Are we dealing with a
D file 		is1D = 0
try to guess [St, xtr] = Remove1DExtension(BrikName)
Opt verb = 1
Opt method = 0
end Opt chunk_size = Opt.SliceSize_1D
Opt chunk_index = Opt.Slices - 1
Opt col_index = Opt.Frames - 1
end end [err, V, Info] = Read_1D(BrikName, Opt)
end Fix the name of the brik
make sure there are no BRIK
or HEAD 		vtmp = findstr(BrikName,'.BRIK')
remove BRIK BrikName = BrikName(1:vtmp(1)-1)
end Now make sure HEAD and
BRIK are present 		sHead = sprintf('%s.HEAD', BrikName)
 sBRIK = sprintf('%s.BRIK', BrikName)
 allslices = 1:Info.DATASET_DIMENSIONS(3)
end isallslices = all(ismember(allslices,Opt.Slices))
 allframes = 1:Info.DATASET_RANK(2)
end isallframes = all(ismember(allframes,Opt.Frames))
found byte order specs
found byte order make sure
it does not conflict with
the user option user specified
a format 		clash
end else did not find ByteOrder
in 		HEAD
end end figure out storage
type 		itype = unique(Info.BRICK_TYPES)
end switch case typestr = 'ubit8'
 fidBRIK = fopen(BrikName, 'rb', Opt.MachineFormat)
end numpix = Info.DATASET_DIMENSIONS(1)*Info.DATASET_DIMENSIONS(2)
 numslices = length(Opt.Slices)
 numframes = length(Opt.Frames)
for k
 istrt = 1+numpix*numslices*(k-1)
 istp = istrt-1+numpix*numslices
else for j
scale if required facs = Info.BRICK_FLOAT_FACS(Opt.Frames)
 iscl = find (facs)
find non zero scales NperBrik = Info.DATASET_DIMENSIONS(1) .* Info.DATASET_DIMENSIONS(2) .* numslices
end end end if required
for i
end colorbar

Function Documentation

colormap (  spectral   ) 
 

Referenced by __glutSetupColormap(), apply_frame(), create_colormap(), Gif_NewXContextFromVisual(), glutGetColor(), main(), and SUMA_ShowAllVisuals().

elseif (  eq_str(Opt.Format,'matrix')   ) 
 

end elseif (  strcmp(Opt.FileFormat, '1D')|strcmp(Opt.FileFormat, '1d')   ) 
 

ErrEval (  FuncName  ,
'Wrn_No Machine Format was specified by user or found in.HEAD file.Using ieee-be(MSB_FIRST)' 
) 
 

found byte order make sure it does not conflict with the user option user specified a format warn ErrEval (  FuncName  ,
'Wrn_Machine format specified conflicts with.HEAD info.Proceeding with fread...' 
) 
 

errordlg (  ErrMessage   ) 
 

end end end end fclose (  fidBRIK   ) 
 

figure (  2   ) 
 

fseek (  fidBRIK  ,
numpix *(slice-1+Info.DATASET_DIMENSIONS(3)*(frame-1))*Info.  TypeBytes,
'bof' 
) 
 

if isallslices fseek (  fidBRIK  ,
numpix *Info.DATASET_DIMENSIONS(3)*(frame-1)*Info.  TypeBytes,
'bof' 
) 
 

Referenced by AFNI_logger(), c_dfe(), c_due(), check_dicom_magic_num(), e_rdue(), e_rsue(), e_wsue(), f__nowreading(), f__nowwriting(), f_back(), f_open(), fseek_(), ge4_read_header(), ge_header(), JMovie2JPEG(), main(), mri_imcount_siemens(), mri_input_delay(), mri_read(), mri_read3D_analyze75(), mri_read_3D(), mri_read_3D_delay(), mri_read_analyze75(), mri_read_siemens(), mri_try_7D(), mri_try_mri(), mri_try_pgm(), mv_cur(), NI_stream_seek(), process_file(), rd_ed(), read_backing_store(), read_ge_header(), read_ge_image(), ReadInputFileNames(), s_wsue(), SUMA_BinarySuck(), SUMA_BrainVoyager_Read(), t_runc(), THD_load_ctfmri(), THD_load_ctfsam(), write_backing_store(), and x_putc().

plot the time course of squeeze is used to turn the x1x1x160 matrix into a x1 vector for the plot function see also WriteBrik The core for this function (  fread and  reshape  ) 
 

if (  exist('spectral')   ) 
 

end end end if reshape V if (  ~  DoVect  ) 
 

if (  ~  isempty(iscl)  ) 
 

if (  Opt.  verbose = = 1  )  = AFNI_OrientCode(NewCode)
 

if (   ) 
 

if (  length(itype)  ,
1 
) 
 

end else did not find ByteOrder in use user option or pick default if (  isempty(Opt.MachineFormat)   ) 
 

found byte order make sure it does not conflict with the user option user specified a format if (  ~  strcmp(Info.ByteOrder, Opt.MachineFormat)  ) 
 

found byte order make sure it does not conflict with the user option if (  ~  isempty(Opt.MachineFormat)  ) 
 

if (  ~  strcmp(Info.ByteOrder,'unspecified')  ) 
 

end if (  ~  filexist(sBRIK)  ) 
 

if (  ~  filexist(sHead)  ) 
 

if (  ~  isempty(vtmp)  ) 
 

end set the format if (  eq_str(Opt.Format,'vector')   ) 
 

end if (  ~  isfield(Opt,'FileFormat')|isempty(Opt.FileFormat)  ) 
 

if (  ~  isfield(Opt,'Frames')|isempty(Opt.Frames)  ) 
 

if (  ~  isfield(Opt,'Slices')|isempty(Opt.Slices)  ) 
 

end if (  ~  isfield(Opt,'Scale')|isempty(Opt.Scale)  ) 
 

end if (  ~  isfield(Opt,'MachineFormat')|isempty(Opt.MachineFormat)  ) 
 

end if (  ~  isfield(Opt,'Format')|isempty(Opt.Format)  ) 
 

end assume you have a brik format and proceed as usual make sure Opt fields are set OK That s done for the new usage format if (  ~  isfield(Opt,'')|isempty(Opt.)  ) 
 

if (  err   ) 
 

if (  isfield(Opt,'Frames')&~isempty(Opt.Frames)   ) 
 

end if (  ~  isfield(Opt, 'SliceSize_1D')|isempty(Opt.SliceSize_1D)  ) 
 

end if (  length(Opt.Slices)~  = 1  ) 
 

end if (  isfield(Opt,'Slices')&~isempty(Opt.Slices)   ) 
 

if (  ~  isfield(Opt, 'method')|isempty(Opt.method)  ) 
 

end if (  is1D   ) 
 

if (  ~  isempty(xtr)  ) 
 

if (  isempty(Opt.FileFormat)   ) 
 

if (  ~  isfield(Opt,'FileFormat')  ) 
 

if (  ~  isstruct(param1)  ) 
 

imagesc (  V(:,:, i, j)   ) 
 

imagesc (  V(:,:, Opt.Slices(i), Opt.Frames(j))   ) 
 

BrikName, [Opt] Purpose:Parameters: (  id  Input,
[,] 2  DATASET_RANK
)  [virtual]
 

end get Brik info and setup for slice and frame selectors (  for  FMRISTAT  ) 
 

size (  V   ) 
 

subplot (  2  ,
2  ,
k 
) 
 

V (  istrt:istp   ) 
 

plot the time course of voxel (  29  ,
33  ,
3 
) 
 

Note that indexing in matlab is different than in AFNI Matlab starts indexing at while AFNI starts with So voxel (  i  ,
j  ,
k 
) 
 

Variable Documentation

allframes = 1:Info.DATASET_RANK(2)
 

Definition at line 244 of file BrikLoad.m.

allslices = 1:Info.DATASET_DIMENSIONS(3)
 

Definition at line 239 of file BrikLoad.m.

plot the time course of squeeze is used to turn the x1x1x160 matrix into a x1 vector for the plot function see also BrikInfo
 

Definition at line 84 of file BrikLoad.m.

end read BRIK file BrikName = BrikName(1:vtmp(1)-1)
 

Definition at line 290 of file BrikLoad.m.

end end case
 

Definition at line 138 of file BrikLoad.m.

Opt chunk_index = Opt.Slices - 1
 

Definition at line 177 of file BrikLoad.m.

end Opt chunk_size = Opt.SliceSize_1D
 

Definition at line 176 of file BrikLoad.m.

found byte order make sure it does not conflict with the user option user specified a format clash
 

Definition at line 255 of file BrikLoad.m.

Opt col_index = Opt.Frames - 1
 

Definition at line 178 of file BrikLoad.m.

Referenced by quantize3_ord_dither(), quantize_ord_dither(), SUMA_AddColAttr(), and SUMA_AddDsetColAttr().

colorbar
 

Definition at line 385 of file BrikLoad.m.

plot the time course of squeeze is used to turn the x1x1x160 matrix into a x1 vector for the plot function see also WriteBrik The core for this NIMH function ReadBRIK Slices and Frames options were added by Dr Keith Worsley for FMRISTAT Marquette University Biophysics Research Medical College of Wisconsin Contact
 

Definition at line 99 of file BrikLoad.m.

Debug Flag DBG = 1
 

Definition at line 109 of file BrikLoad.m.

end set the format DoVect = 0
 

Definition at line 203 of file BrikLoad.m.

end end[err, V, Info] = Read_1D(BrikName, Opt)
 

Definition at line 181 of file BrikLoad.m.

end err = 1
 

Definition at line 349 of file BrikLoad.m.

ErrMessage = ''
 

Definition at line 272 of file BrikLoad.m.

scale if required facs = Info.BRICK_FLOAT_FACS(Opt.Frames)
 

Definition at line 328 of file BrikLoad.m.

fidBRIK = fopen(BrikName, 'rb', Opt.MachineFormat)
 

Definition at line 292 of file BrikLoad.m.

end Opt FileFormat = ''
 

Definition at line 198 of file BrikLoad.m.

see New name of the brik form
 

Definition at line 5 of file BrikLoad.m.

Referenced by memplot_to_topshell(), NI_read_element(), psfile_CB(), r_gr_mk_fill_buttons(), r_HL_mk_buttons(), r_INT_mk_app_buttons(), r_wt_mk_fill_buttons(), SUMA_BrainVoyager_Read_vmr(), SUMA_cb_createSumaCont(), SUMA_cb_createSurfaceCont(), SUMA_CreateDrawROIWindow(), SUMA_CreateTextShell(), SUMA_GuessFormatFromExtension(), SUMA_LoadCmapFile(), SUMA_LoadDset(), SUMA_LoadDsetFile(), SUMA_OpenDX_Read_CruiseVolHead(), SUMA_RemoveDsetExtension(), and SUMA_WriteDset().

Opt Format = 'matrix'
 

Definition at line 41 of file Test_BrikLoad.m.

Referenced by SUMA_SaveDrawnROINIML(), and SUMA_Write_DrawnROI_NIML().

means defined in AFNI doc README attributes Opt Frames = []
 

Definition at line 2070 of file GroupAna.m.

function[err, V, Info, ErrMessage]
 

Initial value:

 BrikLoad (BrikName, param1, param2)
%
%  OLD USAGE for backward compatibility

Definition at line 1 of file BrikLoad.m.

try to guess[St, xtr] = Remove1DExtension(BrikName)
 

Definition at line 153 of file BrikLoad.m.

end else did not find ByteOrder in HEAD
 

Definition at line 262 of file BrikLoad.m.

plot the time course of squeeze is used to turn the x1x1x160 matrix into a x1 vector for the plot function see also WriteBrik The core for this NIMH function ReadBRIK Slices and Frames options were added by Dr Keith Worsley for FMRISTAT http
 

Definition at line 99 of file BrikLoad.m.

for i
 

Initial value:

1:2
   for j=1:2
      k=k+1

Definition at line 381 of file BrikLoad.m.

end get Brik info and setup for slice and frame Info = []
 

Definition at line 237 of file BrikLoad.m.

plot the time course of squeeze is used to turn the x1x1x160 matrix into a x1 vector for the plot function see also Info_1D
 

Definition at line 84 of file BrikLoad.m.

plot the time course of squeeze is used to turn the x1x1x160 matrix into a x1 vector for the plot function see also WriteBrik The core for this NIMH function ReadBRIK Slices and Frames options were added by Dr Keith Worsley for FMRISTAT Marquette University Biophysics Research institute
 

Definition at line 99 of file BrikLoad.m.

end is1D = 0
 

Definition at line 158 of file BrikLoad.m.

end isallframes = all(ismember(allframes,Opt.Frames))
 

Definition at line 248 of file BrikLoad.m.

end isallslices = all(ismember(allslices,Opt.Slices))
 

Definition at line 243 of file BrikLoad.m.

iscl = find (facs)
 

Definition at line 329 of file BrikLoad.m.

istp = istrt-1+numpix*numslices
 

Definition at line 334 of file BrikLoad.m.

Referenced by SUMA_EquateSurfaceSize(), and SUMA_ProjectSurfaceToSphere().

for istrt = 1+numpix*numslices*(k-1)
 

Definition at line 333 of file BrikLoad.m.

Referenced by SUMA_EquateSurfaceSize(), and SUMA_ProjectSurfaceToSphere().

end switch itype = unique(Info.BRICK_TYPES)
 

Definition at line 294 of file WriteBrik.m.

Referenced by EDIT_coerce_autoscale(), EDIT_coerce_autoscale_new(), EDIT_coerce_scale_type(), EDIT_coerce_type(), main(), mkcxcon(), PR_type_scale(), T3D_type_av_CB(), THD_init_datablock_brick(), v1h_put_nc_type(), and v1h_put_NCtype().

for j
 

Initial value:

1:numslices
               slice=Opt.Slices(j)

Definition at line 332 of file BrikLoad.m.

end end end k
 

Initial value:

1:numframes
         frame=Opt.Frames(k)

Definition at line 61 of file RemoveExtension.m.

Referenced by Ado_string(), AffineBruteForceRender(), Argtype(), argverify(), ascii_get_element(), bad_atypes(), balanc_(), balbak_(), bandr_(), bandv_(), binary_get_element(), bisect_(), bqr_(), bup(), c_rotate(), calculate_results(), calculate_ssijk(), calculate_ssijkm(), calculate_ssik(), calculate_ssjk(), calculate_ssk(), calculate_sum(), cbabk2_(), cbal_(), cds(), checkreal(), cinvit_(), cl1_fort(), cl1_solve(), cl1_solve_res(), clset_(), color_init(), color_rotate(), color_swap(), comlr2_(), commonprotos(), compare_SUMA_QSORTROW_FLOAT(), compare_SUMA_QSORTROW_INT(), ComputeScanOffsets(), comqr2_(), consbinop(), copy(), create_colorindex(), create_colormap(), CreateEmptyRLEVoxels(), CreateRLEVoxelsFromRunData(), crunch(), csfft(), csfft_cox(), csfft_many(), csfft_print(), csfft_trigconsts(), ctcell_(), cubic_spline(), DC_gray_change(), DC_gray_conbrio(), DC_gray_contrast(), DC_init_im_gry(), DC_palette_rotate(), DC_palette_swap(), debug_malloc(), debug_malloc_id(), debug_realloc(), debug_realloc_id(), decode_mcu(), decode_mcu_AC_first(), decode_mcu_AC_refine(), do_flip_h(), do_string(), do_uninit_equivs(), docommon(), doentry(), doequiv(), doinclude(), done(), draw_grids(), draw_marker(), DRAW_ttatlas_CB(), draws_(), EDIT_aver_fvol(), EDIT_blur_volume_3d(), EDIT_filter_volume(), encode_mcu_AC_first(), encode_mcu_AC_refine(), encode_one_block(), entry_goto(), eqvcommon(), EvalSpline(), exassign(), expand_array(), ExtractClassifiedVolume(), f__nowwriting(), f_back(), ff_(), fft(), fft128(), fft256(), fft512(), fft64(), FFT_1dcx(), fft_3dec(), fft_4dec(), fft_5dec(), FFT_selection(), fmtname(), fullGtU(), GenerateGrafFunc(), get_fft_mag(), get_line_args(), get_options(), getdimen(), getkwd(), grey_change(), grey_contrast(), grey_init(), grey_rotate(), Haar_ip_FFWT_1d(), Haar_ip_IFWT_1d(), HandleEvent(), hbMakeCodeLengths(), hilbertdelay_V2(), hqr2_(), hqr_(), htest_one_block(), htrib3_(), htribk_(), htrid3_(), htridi_(), identify_repeats(), ifft(), ijk_invwarp(), ijkwarp(), impldcl(), Ims_rot(), imtql2_(), imtqlv_(), inferdcl(), initialize(), InitSpline(), invit_(), ioseta(), legendre(), legendre_(), list_decls(), Load_Any_ind(), Load_Any_RGB(), Load_Next_ind(), Load_Next_RGB(), load_rect_str(), log_2(), main(), make_odither_array(), make_one_const(), malloc(), matrix_check_columns(), matrix_multiply(), matrix_scale(), matrix_singvals(), MatrixMult(), Max_func(), MCW_inverse_histogram_sh(), minfit_(), mkaddr(), mkfunct(), mri_filt_fft(), mri_to_XImage(), mri_watershedize(), neighborCount(), newarg(), node_get_value(), numread(), opconv_fudge(), out_asgoto(), out_const(), p1getf(), ply_put_element(), poly_field(), popinclude(), prconr(), probeDevices(), proto(), put_sub_image_colormap(), putconst(), putentries(), putif(), putpower(), putwhile(), putx(), qh_detjoggle(), qh_detsimplex(), qh_detvnorm(), qh_distnorm(), qh_distplane(), qh_facetarea_simplex(), qh_findbestsharp(), qh_gausselim(), qh_getangle(), qh_getcenter(), qh_gram_schmidt(), qh_init_B(), qh_initflags(), qh_initialhull(), qh_initialvertices(), qh_initqhull_buffers(), qh_initqhull_globals(), qh_initthresholds(), qh_inthresholds(), qh_matchnewfacets(), qh_maxabsval(), qh_maxmin(), qh_maxsimplex(), qh_memsetup(), qh_memsize(), qh_minabsval(), qh_mindiff(), qh_normalize2(), qh_orientoutside(), qh_pointdist(), qh_printafacet(), qh_printcenter(), qh_printcentrum(), qh_printfacet2geom(), qh_printfacet3geom_nonsimplicial(), qh_printfacet3geom_points(), qh_printfacet3geom_simplicial(), qh_printfacet4geom_nonsimplicial(), qh_printfacet4geom_simplicial(), qh_printhelp_singular(), qh_printhyperplaneintersection(), qh_printline3geom(), qh_printmatrix(), qh_printpoint3(), qh_printpointid(), qh_printpointvect(), qh_printstatistics(), qh_printvertex(), qh_printvnorm(), qh_printvoronoi(), qh_projectdim3(), qh_projectinput(), qh_projectpoint(), qh_projectpoints(), qh_randommatrix(), qh_readpoints(), qh_rotatepoints(), qh_scalepoints(), qh_setdelaunay(), qh_setfacetplane(), qh_sethalfspace(), qh_sethyperplane_gauss(), qh_setprint(), qh_voronoi_center(), qzhes_(), qzit_(), qzvec_(), ratqr_(), read_Pfiles(), read_test(), rebak_(), rebakb_(), reduc2_(), reduc_(), reference_fwd_dct(), reference_rev_dct(), REORDER_parseMap(), Resample(), resample(), Resize_Array_Height(), rfft(), save_argtypes(), set_all_surf_vals(), set_surf_results(), set_tmp_names(), setdata(), setfmt(), setintr(), signal_model(), sin_grad(), srface_(), subdivide(), SUMA_assignColors(), SUMA_binTesselate(), SUMA_Chung_Smooth(), SUMA_Chung_Smooth_Weights(), SUMA_ClusterCenterofMass(), SUMA_Cmap_To_SO(), SUMA_ConvexHullSurface(), SUMA_createColGradient(), SUMA_divEdge(), SUMA_dqsortrow(), SUMA_FillToVoxelMask(), SUMA_Find_inIntVect(), SUMA_FindVoxelsInSurface(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_fqsortrow(), SUMA_GetEyeAxis(), SUMA_GetM2M_NN(), SUMA_getoffsets2(), SUMA_getoffsets_ll(), SUMA_GetStandardMap(), SUMA_inNodeNeighb(), SUMA_input(), SUMA_isinbox(), SUMA_isinsphere(), SUMA_isSelfIntersect(), SUMA_isVisibleSO(), SUMA_LoadSpec_eng(), SUMA_M2M_interpolate(), SUMA_MapSurface(), SUMA_MarchingCubesSurface(), SUMA_Mark_Tri(), SUMA_MaskOfNodesInPatch(), SUMA_mattoquat(), SUMA_NI_str_ar_2_comp_str(), SUMA_NodePath_to_TriPath_Inters(), SUMA_OpenDX_Read(), SUMA_Ply_Read(), SUMA_PrepSO_GeomProp_GL(), SUMA_read1D(), SUMA_readColor(), SUMA_RedisplayAllShowing(), SUMA_RegisteredSOs(), SUMA_Search_Min_Dist(), SUMA_SetLocalRemixFlag(), SUMA_SetRemixFlag(), SUMA_SetShownLocalRemixFlag(), SUMA_ShowBrushStroke(), SUMA_Surf_Plane_Intersect(), SUMA_Taubin_Smooth(), SUMA_Taubin_Smooth_Coef(), SUMA_Taubin_Smooth_TransferFunc(), SUMA_UniqueInt(), SUMA_UniqueInt_ind(), SUMA_VisibleSOs(), SUMA_VoxelNeighbors(), SUMA_VoxelsInBox(), SUMA_write1D(), SUMA_writeSpecFile(), SUMA_z_doubqsort(), SUMA_z_dqsort(), SUMA_z_dqsort_nsc(), SUMA_z_qsort(), svd_(), teapot(), THD_autonudge(), THD_dataset_info(), THD_matrix_to_orientation(), tnonc_s2p(), top_nr_name(), tostring(), tql2_(), tqli(), trbak1_(), trbak3_(), trealloc(), tred1_(), tred2(), tred2_(), tred3_(), tridib_(), tsturm_(), type_fixup(), typekludge(), unamstring(), VPCompAC00G(), VPCompAC11B(), VPCompAC1NB(), VPCompAC1NS(), VPCompAC1PB(), VPCompAC31B(), VPCompAC32B(), VPCompAC3NB(), VPCompAC3NS(), VPCompAC3PB(), VPCompAR00G(), VPCompAR11B(), VPCompAR1NB(), VPCompAR1NS(), VPCompAR1PB(), VPCompAR31B(), VPCompAR32B(), VPCompAR3NB(), VPCompAR3NS(), VPCompAR3PB(), VPInitOctreeLevelStack(), VPRenderAffine(), vpSolveSystem4(), wr_ardecls(), wr_array_init(), wr_equiv_init(), wronginf(), x_rsne(), xyz_to_ijk(), and yyparse().

end else did not find ByteOrder in use user option or pick default Opt MachineFormat = ''
 

Definition at line 264 of file BrikLoad.m.

end end Opt method = 0
 

Definition at line 78 of file Read_1D.m.

Referenced by main(), and start_pass().

switch nargin
 

Definition at line 117 of file BrikLoad.m.

find non zero scales NperBrik = Info.DATASET_DIMENSIONS(1) .* Info.DATASET_DIMENSIONS(2) .* numslices
 

Definition at line 330 of file BrikLoad.m.

numframes = length(Opt.Frames)
 

Definition at line 300 of file BrikLoad.m.

end numpix = Info.DATASET_DIMENSIONS(1)*Info.DATASET_DIMENSIONS(2)
 

Definition at line 298 of file BrikLoad.m.

Referenced by int_downsample().

numslices = length(Opt.Slices)
 

Definition at line 299 of file BrikLoad.m.

else Opt = param1
 

Definition at line 70 of file Read_1D.m.

Referenced by calcWithOffsets(), main(), SUMA_3dBRAIN_VOYAGERtoAFNI_ParseInput(), SUMA_3dCRUISEtoAFNI_ParseInput(), SUMA_3dSurfMask_ParseInput(), SUMA_Alloc_Generic_Prog_Options_Struct(), SUMA_Build_Cluster_From_Node(), SUMA_Build_Cluster_From_Node_NoRec(), SUMA_coarsen_ParseInput(), SUMA_ConvexHullSurface(), SUMA_Find_IminImax(), SUMA_FindClusters(), SUMA_FormAfnidset(), SUMA_Free_FormAfniDset_Opt(), SUMA_Free_Generic_Prog_Options_Struct(), SUMA_Get_isosurface_datasets(), SUMA_GimmeSomeSOs(), SUMA_LoadPrepInVol(), SUMA_MarchingCubesSurface(), SUMA_New_FormAfniDset_Opt(), SUMA_OverlaysToOrderedList(), SUMA_PROGRAM_NAME_ParseInput(), SUMA_Reposition_Touchup(), SUMA_SampBias_ParseInput(), SUMA_ScaleToMap(), SUMA_ScaleToMap_alaAFNI(), SUMA_ScaleToMap_Interactive(), SUMA_ScaleToMapOptInit(), SUMA_SkullMask(), SUMA_StretchToFitLeCerveau(), SUMA_Suggest_Touchup(), SUMA_Suggest_Touchup_Grad(), and SUMA_SurfToSurf_ParseInput().

see New name of the brik vector or matrix this is optional
 

Definition at line 5 of file BrikLoad.m.

otherwise
 

Definition at line 145 of file BrikLoad.m.

end end end if required
 

Definition at line 340 of file BrikLoad.m.

return
 

Definition at line 350 of file BrikLoad.m.

sBRIK = sprintf('%s.BRIK', BrikName)
 

Definition at line 223 of file BrikLoad.m.

end Opt Scale = 1
 

Definition at line 167 of file WriteBrik.m.

end Now make sure HEAD and BRIK are present sHead = sprintf('%s.HEAD', BrikName)
 

Definition at line 222 of file BrikLoad.m.

if Opt Slices = []
 

found byte order specs
 

Definition at line 251 of file BrikLoad.m.

case typestr = 'ubit8'
 

Definition at line 302 of file WriteBrik.m.

see New Usage[err, V, Info, ErrMessage]
 

Initial value:

 BrikLoad (BrikName, [form], [MachineFormat])
%
%Purpose:
%   loads an AFNI brik into V
%   
%   
%Input Parameters:
%   BrikName

Definition at line 5 of file BrikLoad.m.

Referenced by main().

else V = []
 

Definition at line 345 of file BrikLoad.m.

else verb = 1
 

Definition at line 79 of file Read_1D.m.

Referenced by clustedit3D(), dump_PBAR_palette_table(), get_octant_clips(), main(), make_peel_mask(), mri_3dalign_method(), mri_automask_image(), mri_brainormalize(), mri_brainormalize_verbose(), mri_medianfilter(), mri_short2mask(), mri_watershedize(), NI_do(), NI_register_doer(), sort_shortvox(), SUMA_Cmap_To_SO(), SUMA_Cmap_To_SO_old(), SUMA_Load1DDset(), SUMA_LoadDset(), SUMA_LoadDXDset(), SUMA_LoadNimlDset(), SUMA_read_ppm(), SUMA_WriteDset(), THD_automask_verbose(), THD_autonudge(), THD_load_datablock(), THD_mask_clust(), THD_mask_erode(), THD_warp3D(), and WINsorize().

end vtmp = findstr(BrikName,'.BRIK')
 

Definition at line 215 of file BrikLoad.m.

 
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