Doxygen Source Code Documentation

GetAfniSlice.m File Reference


Functions
Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to	show (a la AFNI, first slice is indexed 0)%.index is the sub-brick index
AP or RL AP This means that the pixels in slc M go from Right to Left along the st dimension of the	matrix (ie along columns, top to bottom).Pixels go from Anterior to Posterior along the second%dimension of the matrix(ie along rows
turn Brick into a matrix if it isn t already	if (ndims(Brik)< 3)
end	if (~isfield(Opt,'index')\|isempty(Opt.index))
	if (DispManip(iplane).zflip)
	if (nz)
end first grab the slices switch	DispManip (iplane).SliceDim
end first grab the slices switch	for (j=1:1:nz)
end first grab the slices switch slc	M (:,:, j)
Variables
	function [err, slc, slcDisp]
Sa and Co for	axial
Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to default is Output	Parameters
Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to default is Output k being the number of slices requested in Opt i *orientax a x2 character matrix The st and nd rows indicates the orientation of the voxels in the st and nd dimension of	M = zeros(BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(1)), BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(2)), nz)
Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to default is Output k being the number of slices requested in Opt i *orientax a x2 character matrix The st and nd rows indicates the orientation of the voxels in the st and nd dimension of respectively for	example
AP or RL AP This means that the pixels in slc M go from Right to Left along the st dimension of the left to right slcDisp is a structure similar to slc and containing the slices oriented as they would be displayed in AFNI s window Key	Terms
AP or RL AP This means that the pixels in slc M go from Right to Left along the st dimension of the left to right slcDisp is a structure similar to slc and containing the slices oriented as they would be displayed in AFNI s window Key Bethesda Maryland last	modified
Debug Flag	DBG = 1
turn Brick into a matrix if it isn t already	Brik
end initailize return variables	err = 1
switch Opt	plane
switch Opt case	Ax
switch Opt case	iplane = 1
case	Sa
case	Co
end Opt	index = 0
end	indx = Opt.index+1
	DispManip = AFNI_SliceDispManip (BrikInfo)
end	nz = length(Opt.iSlc)
	bufslc = zeros(BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(1)), BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(2)))
end first grab the slices switch	case
this is	inefficient
	return

Function Documentation

end first grab the slices switch DispManip

(

iplane

)

end first grab the slices switch for ( j = 1:1:nz )

end end if

(

)

end if

(

DispManip(iplane).

lrflip

)

end if

(

isfield(Opt,'index')|isempty(Opt.index)

)

turn Brick into a matrix if it isn t already if

(

)

end first grab the slices switch slc M	(	:	,
		:	,
		j
	)

AP or RL AP This means that the pixels in slc M go from Right to Left along the st dimension of the matrix	(	ie along	columns,
		top to	bottom
	)

Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to show	(	a la	AFNI,
		first slice is indexed	0
	)

Referenced by SUMA_OpenDx_Object_Data().

Variable Documentation

switch Opt case Ax

Definition at line 64 of file GetAfniSlice.m.

Sa and Co for axial

Definition at line 1 of file GetAfniSlice.m.

turn Brick into a matrix if it isn t already Brik

Initial value:

 reshape(Brik, BrikInfo.DATASET_DIMENSIONS(1), BrikInfo.DATASET_DIMENSIONS(2),...
                                                BrikInfo.DATASET_DIMENSIONS(3), BrikInfo.DATASET_RANK(2))

Definition at line 58 of file GetAfniSlice.m.

end bufslc = zeros(BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(1)), BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(2)))

Definition at line 116 of file GetAfniSlice.m.

end first grab the slices switch case

Definition at line 97 of file GetAfniSlice.m.

case Co

Definition at line 69 of file GetAfniSlice.m.

Debug Flag DBG = 1

Definition at line 54 of file GetAfniSlice.m.

end end switch DispManip = AFNI_SliceDispManip (BrikInfo)

end initailize return variables err = 1

Definition at line 63 of file GetAfniSlice.m.

Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to default is Output k being the number of slices requested in Opt i* orientax a x2 character matrix The st and nd rows indicates the orientation of the voxels in the st and nd dimension of respectively for example

Definition at line 22 of file GetAfniSlice.m.

function[err, slc, slcDisp]

Initial value:

 GetAfniSlice (Brik, BrikInfo, Opt)
%
%   [err, slc, slcDisp] = GetAfniSlice (Brik, BrikInfo, Opt)
%
%Purpose:
%   Display a slice as it appears in the AFNI window
%   
%   
%Input Parameters:
%   Brik: is a vector or a matrix containing the brik values
%   BrikInfo is a structure containing Header info
%      (both are output by BrikLoad function)
%   Opt is a an options structure with the following fields
%    .plane is the slicing plane. Choose from 'Ax'

Definition at line 1 of file GetAfniSlice.m.

end Opt index = 0

Definition at line 73 of file GetAfniSlice.m.

else indx = Opt.index+1

Definition at line 62 of file WhichSubBricks.m.

Referenced by AFNI_fimmer_compute(), extract_xyz(), fim3d_fimmer_compute(), incbeta(), incbeta_inverse(), indexIntoF(), RT_fim_recurse(), and tnonc_s2p().

this is inefficient

Definition at line 113 of file GetAfniSlice.m.

case iplane = 1

Definition at line 70 of file GetAfniSlice.m.

else slcDisp M = zeros(BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(1)), BrikInfo.DATASET_DIMENSIONS(DispManip(iplane).d(2)), nz)

Definition at line 92 of file GetAfniSlice.m.

AP or RL AP This means that the pixels in slc M go from Right to Left along the st dimension of the left to right slcDisp is a structure similar to slc and containing the slices oriented as they would be displayed in AFNI s window Key Bethesda Maryland last modified

Definition at line 46 of file GetAfniSlice.m.

end nz = length(Opt.iSlc)

Definition at line 84 of file GetAfniSlice.m.

Referenced by activation_region(), adwarp_refashion_dataset(), AFNI_read_images(), AFNI_refashion_dataset(), apply_3shear(), apply_mask(), apply_xshear(), apply_yshear(), apply_zshear(), argmax_(), argnum_(), auto_initialize(), avg_epochs(), center_of_mass(), check_for_valid_inputs(), clustedit3D(), connectivity_tests(), create_row(), create_Tmask(), create_Tmask_byte(), create_Tmask_rgba(), CreatePyramid(), cubic_spline(), DRAW_2D_circle(), DRAW_2D_expand(), DRAW_3D_expand(), DRAW_3D_sphere(), DRAW_into_dataset(), DRAW_receiver(), dset_to_mri(), EDIT_add_bricklist(), EDIT_aver_fvol(), EDIT_blur_volume(), EDIT_blur_volume_3d(), EDIT_filter_volume(), EDIT_main(), EDIT_one_dataset(), EDIT_volpad(), estimate_field(), estimate_gfw(), estpdf_initialize(), eval_registration(), extract_byte_speedtest(), find_extrema(), find_local_maxima(), flip_xy(), flip_xz(), flip_yz(), gaussian_filter(), generate_image(), get_activation_region(), get_best_shift(), get_octant_clips(), get_options(), HISTO_main(), identify_clusters(), IMREG_main(), initialize(), initialize_options(), initialize_program(), main(), make_peel_mask(), MCW_build_mask(), MCW_erode_clusters(), MCW_find_clusters(), MCW_scale_to_max(), MCW_vol_amax(), mri_3dalign_edging_default(), mri_3dalign_setup(), MRI_5blur_inplace_3D(), MRI_autobbox(), mri_automask_image(), mri_brainormalize(), mri_get_cmass_3D(), mri_imcount(), mri_imcount_analyze75(), mri_imcount_dicom(), mri_medianfilter(), mri_new_7D_generic(), mri_new_vol(), mri_new_vol_empty(), mri_read3D_analyze75(), mri_read_3A(), mri_read_3D(), mri_read_3D_delay(), mri_read_analyze75(), mri_read_dicom(), mri_read_siemens(), mri_short2mask(), mri_try_7D(), mri_warp3D_align_edging_default(), mri_warp3d_align_one(), mri_warp3D_align_setup(), mri_warp3D_cubic(), mri_warp3D_get_delta(), mri_warp3D_linear(), mri_warp3D_NN(), mri_warp3D_quintic(), mri_warp3D_resize(), mri_watershedize(), NIH_find_clusters(), niml_to_mri(), output_results(), partial_cliplevel(), PC_read_opts(), pcalc(), pfit(), poly_field(), populate_nifti_image(), process_all_datasets(), process_as_floats(), process_data(), project_byte_mip(), r_fill_resampled_data_brick(), r_index2pt(), r_INT_cb_fill(), r_mri_read_dicom(), r_wt_set_neighbors(), RCREND_cutout_blobs(), RCREND_load_dsl(), RCREND_reload_func_dset(), RCREND_xhair_overlay(), RCREND_xhair_underlay(), read_afni_data(), remove_field(), remove_isolated_stuff(), REND_cutout_blobs(), REND_load_dsl(), REND_reload_func_dset(), REND_xhair_overlay(), REND_xhair_underlay(), ROIPLOT_main(), RT_registration_2D_close(), RT_registration_2D_onevol(), RT_registration_2D_setup(), RT_registration_3D_setup(), segment_envelope(), segment_x_slices(), segment_y_slices(), segment_z_slices(), STAVG_main(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_FormAfnidset(), SUMA_isSkin(), SUMA_make_vnlist(), SUMA_SurfGridIntersect(), swaptest(), T3D_fix_dataset_dimen(), T3D_read_images(), T3D_swap_CB(), T3D_type_av_CB(), target_into_dataset(), THD_3dim_dataset_to_brick(), THD_datablock_apply_atr(), THD_datablock_from_atr(), THD_dataset_rowfillin(), THD_dataset_zfillin(), THD_get_dset_row(), THD_init_datablock_brick(), THD_load_analyze(), THD_load_ctfmri(), THD_load_ctfsam(), THD_load_datablock(), THD_load_minc(), THD_load_mpeg(), THD_load_nifti(), THD_mask_clip_neighbors(), THD_mask_clust(), THD_mask_dilate(), THD_mask_distize(), THD_mask_erode(), THD_mask_fillin_completely(), THD_mask_fillin_once(), THD_open_analyze(), THD_open_ctfmri(), THD_open_ctfsam(), THD_open_mpeg(), THD_orient_guess(), THD_peel_mask(), THD_put_dset_row(), THD_rota_vol(), THD_rota_vol_2byte(), THD_rota_vol_byte(), THD_rota_vol_matvec(), THD_rota_vol_matvec_2byte(), THD_set_dataset_attributes(), THD_write_1D(), THD_write_datablock(), threshold_data(), TT_whereami(), voldif(), vpNormal(), vpNormalIndex(), vpShadeTable(), warp_image(), WINsorize(), write_bucket(), and zedit_mask().

Sa and Co for sagittal and coronal iSlc is an Nx1 vector with slice indices to default is Output Parameters

Definition at line 22 of file GetAfniSlice.m.

switch Opt plane

Definition at line 64 of file GetAfniSlice.m.

return

Definition at line 123 of file GetAfniSlice.m.

case Sa

Definition at line 67 of file GetAfniSlice.m.

Definition at line 46 of file GetAfniSlice.m.

AFNI/NIfTI Server

Sections

Personal tools

Navigation

Doxygen Source Code Documentation

GetAfniSlice.m File Reference

Functions

Variables

Function Documentation

Variable Documentation