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ContrVec.m File Reference

Go to the source code of this file.


Functions

switch order dmat (:, num_col0+1:num_col0+num_col(1)) is the matrix for 1st order contrasts for(i
and no of arrows in dmat Contr
ord1 		cnt (i).scalar=0
 for (j=1:1:Contr.ord1.cnt(i).NT)
Grand mean for (k=1:1:NF)
Grand mean if (Contr.ord1.cnt(i).code(j).str(k) >= 'a'&Contr.ord1.cnt(i).code(j).str(k)<= 'z')
i k ()
 elseif (first > 1)
 fprintf ('\nError in contrast coding:more than one non-zero index in 1st order constrasts!\n')
 fprintf (2,'Halted:Ctrl+c to exit')
end if (first==1) end%if(tmpv~=0) end%for(k
end end if (Contr.ord1.cnt(i).code(j).str(Contr.ord1.cnt(i).idx1) >= 'a'&Contr.ord1.cnt(i).code(j).str(Contr.ord1.cnt(i).idx1)<= 'z')
 for (ll=1:1:n)%Should have a more decent way to do this in a matrix fashion instead of a lenthy loop?tmpstr
if strcmp (tmpstr, FL(Contr.ord1.cnt(i).idx1).level(tmpv).expr) count
j count ()
assuming balanced design end for (i=1:1:Contr1.tot) case 2
assuming balanced design end dmat (:, num_col0+num_col(1)+1:num_col0+num_col(1)+num_col(2)) is the matrix for 2nd order contrasts%when the 1st factor is collapsed%shift1
1, n zeros ()
id first ()
 if (Contr.ord2.cnt(i).code(j).str(k) >= 'a'&Contr.ord2.cnt(i).code(j).str(k)<= 'z')
end if (tmpv~=0)
 elseif (first==2)
id contrasts: (i idx2)
 if (Contr.ord2.cnt(i).code(j).str(1) >= 'a'&Contr.ord2.cnt(i).code(j).str(1)<= 'z')
end if (Contr.ord2.cnt(i).code(j).str(sec_fctr) >= 'a'&Contr.ord2.cnt(i).code(j).str(sec_fctr)<= 'z')
 if (sec_fctr > 2)
end if (Contr.ord2.cnt(i).code(j).str(2) >= 'a'&Contr.ord2.cnt(i).code(j).str(2)<= 'z') = 10 + Contr.ord2.cnt(i).code(j).str(2) - 'a'
end if (Contr.ord2.cnt(i).code(j).str(3) >= 'a'&Contr.ord2.cnt(i).code(j).str(3)<= 'z')
end if (Contr.ord2.cnt(i).code(j).str(4) >= 'a'&Contr.ord2.cnt(i).code(j).str(4)<= 'z')
i idx2 ()
end if (sec_fctr > 3)
end if (NF==3)
else fprintf ('\nSomething is wrong in the contrast coding!\n')
3 a ()
end if (sec_fctr > 4)
end if (sec_fctr > 5)
if strcmp (tmpstr1, FL(Contr.ord2.cnt(i).idx1).level(tmpv1).expr)&strcmp(tmpstr2
if FL (Contr.ord2.cnt(i).idx2).level(tmpv2).expr) count
 if (Contr.ord3.cnt(i).code(j).str(k) >= 'a'&Contr.ord3.cnt(i).code(j).str(k)<= 'z')
k str ()

Variables

 function [err, Contr]
Bethesda MD Define the function
name for easy referencing 		FuncName = 'ContrVec.m'
Debug Flag DBG = 1
initialize return variables err = 1
switch order case
 n = ntot in anovan.m: total number of files
for each term in a contrast first = 0
 shift = 1
Grand mean tmpv = 10 + Contr.ord1.cnt(i).code(j).str(k) - 'a'
 tmp = FL(k).N_level
 pause
 count = 0
The part should be valid for
both balanced and unbalanced
designs 		tmpstr = char (group{Contr.ord1.cnt(i).idx1})
For variance coef
when the nd factor is collapsed shift2 = (FL(2).N_level*(FL(3).N_level + FL(4).N_level))*(str2num(Contr2.cnt(i).code(1).str(2)) == 0)
when the rd factor is collapsed shift3 = (FL(3).N_level*FL(4).N_level)*(str2num(Contr2.cnt(i).code(1).str(3)) == 0)
when the th factor is collapsed shift4 = FL(4).N_level*(str2num(Contr2.cnt(i).code(1).str(4)) == 0)
 tmpv1 = 10 + Contr.ord2.cnt(i).code(j).str(1) - 'a'
end tmpv2 = 10 + Contr.ord2.cnt(i).code(j).str(sec_fctr) - 'a'
shift over AB
shift over AC
 tmpstr2 = char (group{Contr.ord2.cnt(i).idx2}(ll))
skip grand mean

Function Documentation

3 a (   )  [virtual]
 

and no of arrows in dmat Contr ord1 cnt (  i   )  [pure virtual]
 

id contrasts: (  i  idx2  )  [virtual]
 

j count (   )  [virtual]
 

assuming balanced design end dmat (  :  ,
num_col0+  num_col(1)+1:num_col0+num_col(1)+num_col(2)
) 
 

switch order dmat (  :  ,
num_col0+1:num_col0+  num_col(1)
) 
 

level elseif (  first  = = 2  ) 
 

elseif (  first  ,
1 
) 
 

id first (   )  [virtual]
 

if FL (  Contr.ord2.cnt(i).  idx2  ) 
 

Referenced by SUMA_Make_Edge_List(), SUMA_Make_Edge_List_eng(), SUMA_MakeConsistent(), and SUMA_Take_A_Hike().

assuming balanced design end for (  i  = 1:1:Contr1.tot  ) 
 

for (  ll  = 1:1:n  ) 
 

Grand mean for (  k  = 1:1:NF  ) 
 

for (  j  = 1:1:Contr.ord1.cnt(i).NT  ) 
 

else fprintf (  '\nSomething is wrong in the contrast coding!\n'   ) 
 

fprintf (  2  ,
'Halted:Ctrl+c to exit' 
) 
 

fprintf (  '\nError in contrast coding:more than one non-zero index in 1st order constrasts!\n'   ) 
 

i idx2 (   )  [virtual]
 

if (  Contr.ord3.cnt(i).code(j).str(k) >= 'a'&Contr.ord3.cnt(i).code(j).str(k)<= 'z'   ) 
 

end if (  sec_fctr  ,
5 
) 
 

end if (  sec_fctr  ,
4 
) 
 

end end end end if (  NF  = = 3  ) 
 

Initial value:

= 5),   

   % 1st order contrasts
   flg = 0

end if (  sec_fctr  ,
3 
) 
 

end if (  Contr.ord2.cnt(i).code(j).str(4) >= 'a'&Contr.ord2.cnt(i).code(j).str(4)<= 'z'   ) 
 

end if (  Contr.ord2.cnt(i).code(j).str(3) >= 'a'&Contr.ord2.cnt(i).code(j).str(3)<= 'z'   ) 
 

if (  Contr.ord2.cnt(i).code(j).str(2) >= 'a'&Contr.ord2.cnt(i).code(j).str(2)<= 'z'   )  = 10 + Contr.ord2.cnt(i).code(j).str(2) - 'a'
 

if (  sec_fctr  ,
2 
) 
 

end if (  Contr.ord2.cnt(i).code(j).str(sec_fctr) >= 'a'&Contr.ord2.cnt(i).code(j).str(sec_fctr)<= 'z'   ) 
 

AC AD if (  Contr.ord2.cnt(i).code(j).str(1) >= 'a'&Contr.ord2.cnt(i).code(j).str(1)<= 'z'   ) 
 

end if (  tmpv~  = 0  ) 
 

if (  Contr.ord2.cnt(i).code(j).str(k) >= 'a'&Contr.ord2.cnt(i).code(j).str(k)<= 'z'   ) 
 

end end if (  Contr.ord1.cnt(i).code(j).str(Contr.ord1.cnt(i).idx1) >= 'a'&Contr.ord1.cnt(i).code(j).str(Contr.ord1.cnt(i).idx1)<= 'z'   ) 
 

end if (  first  = =1  )  [pure virtual]
 

Grand mean if (  Contr.ord1.cnt(i).code(j).str(k) >= 'a'&Contr.ord1.cnt(i).code(j).str(k)<= 'z'   ) 
 

i k (   )  [virtual]
 

k str (   )  [virtual]
 

if strcmp (  tmpstr1  ,
FL(Contr.ord2.cnt(i).idx1).level(tmpv1).  expr
) 
 

if strcmp (  tmpstr  ,
FL(Contr.ord1.cnt(i).idx1).level(tmpv).  expr
) 
 

n zeros (   )  [virtual]
 

Variable Documentation

shift over AB
 

Definition at line 146 of file ContrVec.m.

shift over AC
 

Definition at line 146 of file ContrVec.m.

end case
 

Definition at line 219 of file ContrVec.m.

For variance coef
 

Definition at line 285 of file ContrVec.m.

count = 0
 

Definition at line 82 of file ContrVec.m.

Debug Flag DBG = 1
 

Definition at line 35 of file ContrVec.m.

initialize return variables err = 1
 

Definition at line 38 of file ContrVec.m.

end first = 0
 

Definition at line 308 of file ContrVec.m.

Referenced by __glutProcessDeviceEvents(), AFNI_define_CB(), AFNI_force_adoption(), AFNI_setup_viewing(), clock_time(), Clp_SetOptionChar(), COX_clock_time(), csfft_cox(), detrend(), E0001(), EDIT_filter_volume(), EXP0D_worker(), gaudf(), glutBitmapCharacter(), glutBitmapLength(), glutBitmapWidth(), init_colors(), iochan_init(), main(), MCW_alter_widget_cursor(), MCW_choose_CB(), MCW_popup_message(), mpeg_setup(), mri_read_stuff(), multivector_read(), NI_clock_time(), PBAR_enviro_bigmaps(), plot_graphs(), PLUTO_elapsed_time(), PNMtoYUV(), PPMtoYUV(), ranco(), read_compressed_image(), read_URL_http(), RT_worker(), RWC_drag_circle(), RWC_drag_rectangle(), RWC_xineramize(), slist_choose_surfs(), SPLASH_decodexx(), T3D_quit_CB(), T3D_read_images(), tabletPosChange(), THD_datablock_from_atr(), THD_write_minc(), tross_multi_Append_History(), unif_(), volume_search(), VPComputeDepthCueTable(), waveform_EXPR(), write_formats(), and yylex().

Bethesda MD Define the function name for easy referencing FuncName = 'ContrVec.m'
 

Definition at line 32 of file ContrVec.m.

function[err, Contr]
 

Initial value:

 ContrVec(order, n, NF, group, dmat, Contr, FL, num_col)
%
%   [err,] = ContrVec.m ()
%
%Purpose:
%   
%   Obtain a vector for each contrast so that effect size is calculated in SumsOfSquares.m
%   
%Input Parameters:
%   
%   
%   
%Output Parameters:
%   err : 0 No Problem
%       : 1  Problems
%   
%   
%      
%Key Terms:
%   
%More Info :
%   
%   
%   
%
%     Author : Gang Chen
%     Date : Wed Dec 1 10:15:29 EST 2004
%     SSCC/NIMH/ National Institutes of Health

Definition at line 1 of file ContrVec.m.

skip grand mean
 

Definition at line 293 of file ContrVec.m.

Referenced by calc_covariance(), calculate_ameans(), calculate_bmeans(), calculate_cmeans(), calculate_means(), calculate_xmeans(), cdfnor(), corcol(), covcol(), do_stats(), EDIT_cluster_array(), EDIT_filter_volume(), initialize(), main(), mean_array(), normal(), normal_p2t(), normal_t2p(), SUMA_FindClusters(), and threshold_data().

n = ntot in anovan.m: total number of files
 

Definition at line 296 of file ContrVec.m.

pause
 

Definition at line 271 of file ContrVec.m.

Referenced by s_paus().

assuming balanced design end shift = 1
 

Definition at line 293 of file ContrVec.m.

Referenced by copy_chunk(), get_best_shift(), Gif_ClipImage(), mkbitcon(), mri_read_dicom(), mri_shift_1D(), qh_scalelast(), qh_scalepoints(), shifter(), skip_chunk(), and wrt_E().

when the nd factor is collapsed shift2 = (FL(2).N_level*(FL(3).N_level + FL(4).N_level))*(str2num(Contr2.cnt(i).code(1).str(2)) == 0)
 

Definition at line 102 of file ContrVec.m.

when the rd factor is collapsed shift3 = (FL(3).N_level*FL(4).N_level)*(str2num(Contr2.cnt(i).code(1).str(3)) == 0)
 

Definition at line 104 of file ContrVec.m.

when the th factor is collapsed shift4 = FL(4).N_level*(str2num(Contr2.cnt(i).code(1).str(4)) == 0)
 

Definition at line 107 of file ContrVec.m.

intensity for this rd order contrast tmp = FL(k).N_level
 

Definition at line 750 of file SumsOfSquares.m.

Referenced by argmax_(), bsort_(), c_padd(), calc_good_fit(), DCM_GetString(), DELAY_tsfuncV2(), do_stats(), drawBox(), extract_index(), EXTRACT_tsfunc(), extract_xyz(), F2D_chainfunc(), fileExists(), finalize_sequence(), generateMTFValues(), get_dqt(), get_dri(), getAndMoveToFrontDecode(), GIF_Get_Code(), hilbertdelay_V2(), hunwrap(), idct_row(), LumMotionError(), mad_(), main(), matrix_inverse(), mean_(), median_(), motion_fi_conceal(), motion_fr_conceal(), MResize(), mri_medianfilter(), mse(), NC_lookupattr(), nc_rename_att(), padd(), Parse_Specifics_File_v2(), per_scan_setup(), processEvents(), r_dxyz_mod_dataxes(), r_index2pt(), ReadInputFileNames(), readPreamble(), recvDecodingTables(), reference_fwd_dct(), reference_rev_dct(), sendMTFValues(), set_3dmm_bounds(), snocString(), sort_shortvox(), SpecLookup(), SpecTypeLookup(), STATS_tsfunc(), stdev_(), SUMA_Build_Cluster_From_Node(), SUMA_Build_FirstNeighb(), SUMA_cb_DrawROI_Redo(), SUMA_cb_DrawROI_Undo(), SUMA_CreateTable(), SUMA_EquateSurfaceSize(), SUMA_Find_inIntVect(), SUMA_Mesh_IJK_nel2Mesh_IJK(), SUMA_nimlSO2SO(), SUMA_NodeXYZ_nel2NodeXYZ(), SUMA_process_NIML_data(), SUMA_ProjectSurfaceToSphere(), SUMA_RemoveDsetExtension(), SUMA_RemoveSurfNameExtension(), SUMA_VolPar_nel2SOVolPar(), swap_4(), swapATGroupElement(), swapInPlace(), TT_whereami(), undoReversibleTransformation_small(), v2s_apply_filter(), VPLoadRotation(), vpMultMatrix(), vpRotate(), vpScale(), vpTranslate(), vpWindow(), and WINsorize().

The part should be valid for both balanced and unbalanced designs tmpstr = char (group{Contr.ord1.cnt(i).idx1})
 

Definition at line 83 of file ContrVec.m.

Referenced by DELAY_main(), EXTRACT_main(), main(), SUMA_cb_createSurfaceCont(), SUMA_Init_SurfCont_SurfParam(), and SUMA_InitializeColPlaneShell().

tmpstr2 = char (group{Contr.ord2.cnt(i).idx2}(ll))
 

Definition at line 277 of file ContrVec.m.

else tmpv = 10 + Contr.ord1.cnt(i).code(j).str(k) - 'a'
 

Definition at line 305 of file ContrVec.m.

Referenced by vpShadeTable(), and vpSolveSystem4().

else tmpv1 = 10 + Contr.ord2.cnt(i).code(j).str(1) - 'a'
 

Definition at line 245 of file ContrVec.m.

else tmpv2 = 10 + Contr.ord2.cnt(i).code(j).str(sec_fctr) - 'a'
 

Definition at line 248 of file ContrVec.m.

 
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