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Doxygen Source Code Documentation
SumsOfSquares.m File Reference
Go to the source code of this file.
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Functions |
| | SS (Error) |
| get its residual SS and d f | ssw (1:nterms) |
| end if | dfboth (k0)~ |
| | ssw (k) |
| | sswo (k) |
| | ssterm (dfterm==0)=0 |
| | C (A) |
| | BC (A) ssterm(3) |
| | SSC (A) |
| | SSBC (A) |
| | CD (ABC) |
| | ssterm (4) |
| | SSD (A) |
| | DF (D(A)) |
| | SSBD (A) |
| | DF (BD(A)) |
| | SSCD (A) |
| | DF (CD(A)) |
| | SSBCD (A) |
| | DF (BCD(A)) |
| | DF (D(AB)) |
| | DF (CD(AB)) |
| id | terms: (A) |
| | DE (ABC) |
| | ABDE (ACDE) |
| only terms | ssterm (5) |
| | SSE (A) |
| | DF (E(A)) |
| | SSBE (A) |
| | DF (BE(A)) |
| | SSCE (A) |
| | DF (CE(A)) |
| | SSDE (A) |
| | DF (DE(A)) |
| | SSBCE (A) |
| | DF (BCE(A)) |
| | SSBDE (A) |
| | DF (BDE(A)) |
| | SSCDE (A) |
| | DF (CDE(A)) |
| | SSBCDE (A) |
| | DF (BCDE(A)) |
Throw out those four which
do not exist for | intensity (6)] |
| | tnames (6)] |
| 6 | dfe () |
| | tnames (8:11) |
| | tnames (14)] |
| | tnames (8) |
| | tnames (10:11)] |
| denominator | dfterm (4) |
| denominator | dfterm (10) |
| | tnames (10:17) |
| | tnames (19) |
| | tnames (22:26) |
| | tnames (30)] |
Only calculate it when denominator
is greater than | fstat (t) |
assign this so that output
argument LC would not be empty
else | if (NF==1) |
| | if (tmp > 0) |
| LC | t1 (i).t |
end end end Get t values for
contrast | tests (B) |
| ABC | for (i=1:1:Contr.ord2.tot) |
| ABC LC | t2 (i).t=0 = LC.t2(i).value/sqrt(tmp) |
initializtion in case it is
assigned later on due to denominator
of switch Contr ord2 | cnt (i).idx1 case 1 |
| A | BXC: (dsgn==3|dsgn==4 msdenom) |
| MSBC else | fprintf ('\nSomething is wrong in the contrast coding!\n') |
| | fprintf (2,'Halted:Ctrl+c to exit') |
| end end end | if (Contr.ord2.tot > 0) |
| end end end | dmat (:, num_col0+num_col1+1:num_col1+num_col0+num_col2) is the matrix for 2nd order contrasts if(Contr.ord3.tot > 0) |
| end end end LC | t3 (i).t=0 = Contr.ord3.cnt(i).vec * y0 |
initializtion in case it is
assigned later on due to denominator
of switch Contr ord3 switch
Contr ord3 | if (Contr.ord3.cnt(i).idx3==3) |
| end end end end | If (NF==3) if(NF |
Less likely each term of this
contrast | LC2 (i).value = LC2(i).value + Contr2.cnt(i).coef(j) * dmat(:, Contr2.cnt(i).code(j).pos)' * y0 |
initializtion in case it is
assigned later on due to denominator
of | if (dsgn==3) |
| MSABD not exist | for (dsgn==3|dsgn==4|dsgn==5) end case 3 |
end end end Get t values for
contrast tests within each | factor (B) |
| | elseif (dsgn==3) what |
| end end LC | t4 (i).t=0 = LC.t4(i).value/sqrt(tmp) |
| MSABCE end switch Contr ord4 | if (Contr.ord4.cnt(i).idx4==5) |
Variables |
| | function [err, fstat, intensity_new, dfterm_new, dfdenom, tnames_new, LC] |
which are defined as the sqare
root of MS terms | dfterm |
which are defined as the sqare
root of MS terms Bethesda
MD Define the function name
for easy referencing | FuncName = 'ss.m' |
| Debug Flag | DBG = 1 |
| initailize return variables | err = 1 |
| | dfboth = dfbothSS |
| | y0 = y |
y gets mutated down below
Keep the original y so that
the contrasts can be done
later at the end Fit the full
model and compute the residual
sum of squares | mu = mean(y) |
| | y = y - mu |
| two passes to improve accuracy | mu2 = mean(y) |
| | sst = sum(y.^2) |
| | SSTO [ssx, y] = dofit(y, Qd) |
| y | __pad3__ |
| ssx | __pad4__ |
for full model we already
know the results for | j |
Look in unsorted arrays to
see if we have already fit
this model if j nterms | k0 = k+nterms |
| else | thismod = modw(k, :) |
| end Fit this | model [ssx0, dfx0] = QRfit(X, y, C) |
| | ssx0 = dofit(y, s(j).Qdt) |
Use these results for each
term that requires them | mod0 = repmat(thismod, nterms, 1) |
| | k = find(all(modw == mod0, 2)) |
end clear mod0 Compute the
sum of squares attributed
to each term | ssterm = ssw - sswo |
| make this | exact |
| make this | fstat = repmat(0, size(ssterm)) |
| only ss | term |
| | case |
| terms | __pad5__ |
| | B |
| | C |
| | AB |
| | AC |
| | BC |
end switch dsgn switch dsgn
Order of the | terms |
| | D |
| | AD |
| | BD |
| | ABD |
| | ACD |
| | BCD |
| and | ABCD |
| | CD |
| | ABC |
| | E |
| | AE |
| | BE |
| | CE |
| | ABE |
| | ACE |
| | ADE |
| | BCE |
| | BDE |
| | CDE |
| | ABCE |
| | BCDE |
end switch dsgn end switch
NF Compute the mean square
for each term | msterm = ssterm ./ max(1, dfterm') |
| | mse = sse * (dfe>0) / max(1, dfe) |
| | intensity = sqrt(msterm) |
Intensity for each term Equated
computed and expected mean | squares |
Intensity for each term Equated
computed and expected mean
then solve for variance component
estimates switch NF | dfterm_new = dfterm |
| | tnames_new = tnames |
| | msterm_new = msterm |
| | intensity_new = intensity |
| | msdenom = repmat(mse, size(msterm)) |
| | dfdenom = repmat(dfe, size(msterm)) |
| terms | __pad6__ |
| terms | __pad7__ |
Throw out those four which
do not exist for | nesting |
| terms | __pad8__ |
| denominator | MS |
| denominator | dfe |
denominator DF end end Close
swtich NF Compute an F statistic
for each term | t = (msdenom>0) |
| | LC = 0 |
assign this so that output
argument LC would not be empty
else Get t values for contrast
tests within each factor(1st order)%dmat(initializtion
in case it is assigned later
on due to denominator of LC | t1 (i).value = Contr.ord1.cnt(i).vec * y0 |
intensity for this st order
contrast | tmp = msdenom(Contr.ord1.cnt(i).idx1)*Contr.ord1.cnt(i).scalar |
initializtion in case it is
assigned later on due to denominator
of switch Contr ord2 switch
Contr ord2 | what = msdenom(4) |
| | pause |
| Less likely to | occur |
| | scalar = scalar + Contr2.cnt(i).coef(j) * Contr2.cnt(i).coef(j) |
| | return |
Function Documentation
| A BXC: |
( |
dsgn |
= =3|dsgn==4 msdenom |
) |
[virtual] |
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| initializtion in case it is assigned later on due to denominator of switch Contr ord2 cnt |
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| denominator dfterm |
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10 |
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Referenced by adjust_endpts(), assign_afni_floats(), attach_sub_brick(), basis_write_iresp(), basis_write_sresp(), calculate_acontrasts(), calculate_adifferences(), calculate_ameans(), calculate_bcontrasts(), calculate_bdifferences(), calculate_bmeans(), check_for_valid_inputs(), DepthCueSlice(), display_coords(), mask_all_shorts_to_float(), mask_shorts_to_float(), mri_to_mri_scl(), process_as_floats(), process_subbrick(), qh_voronoi_center(), r_set_afni_s_from_dset(), rfft(), thd_mask_from_brick(), v2s_adjust_endpts(), write_3dtime(), write_bucket_data(), and write_ts_array(). |
| MSABD not exist for |
( |
dsgn |
= = 3 | dsgn == 4 | dsgn == 5 |
) |
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| fprintf |
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2 |
, |
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'Halted:Ctrl+c to exit' |
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| Only calculate it when denominator is greater than fstat |
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t |
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| MSABCE end switch Contr ord4 if |
( |
Contr.ord4.cnt(i). |
idx4 = = 5 |
) |
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| initializtion in case it is assigned later on due to denominator of if |
( |
dsgn |
= = 3 |
) |
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| initializtion in case it is assigned later on due to denominator of switch Contr ord3 switch Contr ord3 if |
( |
Contr.ord3.cnt(i). |
idx3 = = 3 |
) |
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| Throw out those four which do not exist for intensity |
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6 |
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| Less likely each term of this contrast LC2 |
( |
i |
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= LC2(i).value + Contr2.cnt(i).coef(j) * dmat(:, Contr2.cnt(i).code(j).pos)' * y0 |
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| ssterm |
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dfterm |
= =0 |
) |
[pure virtual] |
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| LC t2 |
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i |
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= LC.t2(i).value/sqrt(tmp) [pure virtual] |
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Referenced by add_quats(), alnrel(), basis_block_hrf4(), basis_block_hrf5(), bgrat(), bisect_(), calc_glt_matrix(), cx_scramble(), dln1px(), fft128(), fft256(), fft512(), fft64(), fft_3dec(), fft_4dec(), get_quadratic_trend(), idct_col(), idct_row(), InvertSym3(), maxtype(), median_float4(), PERMTEST_compute(), putpower(), qzvec_(), stas4(), SUMA_Find_IminImax(), SUMA_FindVoxelsInSurface(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_isinbox(), SUMA_isinsphere(), SUMA_isSelfIntersect(), SUMA_StretchToFitLeCerveau(), THD_cubic_detrend(), tridib_(), tsturm_(), and UTL_SqueezeBlanks(). |
| LC t3 |
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= Contr.ord3.cnt(i).vec * y0 [pure virtual] |
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| LC t4 |
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= LC.t4(i).value/sqrt(tmp) [pure virtual] |
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| id terms: |
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A |
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[virtual] |
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Variable Documentation
| Throw out those four which do not exist for ACD |
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| denominator MS dfdenom = repmat(dfe, size(msterm)) |
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| fstat = repmat(0, size(ssterm)) |
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Initial value: SumsOFSquares(y, NF, FL, ntot, nterms, Qd, s, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, dsgn, N_Brik, Contr)
%
% [err,] = ss.m ()
%
%Purpose:
%
%
%
%Input Parameters:
%
% y: values from all factor combinations at one voxel in vector format
% ntot: total number of files = length of vector y
% tername: term names such as
% termlist:
% dmat: design matrix in the converted regression model
% cmat: constraints matrix
%
%Output Parameters:
% err : 0 No Problem
% : 1 Problems
% fstat: a vector of F values for those terms at a voxel
% intensity_new: intensity for those terms at a voxel
Definition at line 1 of file SumsOfSquares.m. |
| Only preserve those valid for nesting Semicolon for coloumn catenation msdenom = repmat(mse, size(msterm)) |
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| mse = sse * (dfe>0) / max(1, dfe) |
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| end switch dsgn end switch NF Compute the mean square for each term msterm = ssterm ./ max(1, dfterm') |
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| two passes to improve accuracy mu2 = mean(y) |
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| denominator DF end end Close swtich NF Compute an F statistic for each term t = (msdenom>0) |
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Referenced by add_quats(), basis_block_hrf4(), basym(), bisect_(), calc_glt_matrix(), ComputeD0(), cx_scramble(), fft128(), fft256(), fft512(), fft64(), fft_3dec(), fft_4dec(), get_linear_trend(), get_quadratic_trend(), gratio(), idct_col(), idct_row(), Inline(), maxtype(), median_float4(), putcall(), putpower(), qzvec_(), rcomp(), shear_xzyx(), stas4(), SUMA_FindVoxelsInSurface(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_isinbox(), SUMA_isinsphere(), SUMA_isSelfIntersect(), THD_cubic_detrend(), tridib_(), tsturm_(), UTL_SqueezeBlanks(), VPCompAC00G(), VPCompAC11B(), VPCompAC1NB(), VPCompAC1NS(), VPCompAC1PB(), VPCompAC31B(), VPCompAC32B(), VPCompAC3NB(), VPCompAC3NS(), VPCompAC3PB(), VPCompAR00G(), VPCompAR11B(), VPCompAR1NB(), VPCompAR1NS(), VPCompAR1PB(), VPCompAR31B(), VPCompAR32B(), VPCompAR3NB(), VPCompAR3NS(), VPCompAR3PB(), VPRenderAffine(), and vpShadeTable(). |
| THIS CAN BE DELETED FOR MY CASE since it is not used from this point y = y - mu |
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Definition at line 49 of file SumsOfSquares.m.
Referenced by bratio(), brcmp1(), brcomp(), ClassifyRawVolume(), ComputeOctreeMask(), dbesy0_(), drawBox(), ExtractClassifiedVolume(), ExtractRawVolume(), mri_drawline(), plx_TXT(), pointclip(), POWER_main(), ppmd_circle(), ppmd_line(), ppmd_polyspline(), ppmd_spline3(), ShadeRawVolume(), SUMA_DrawWindowLine(), VPClassifyBlock(), vpExtract(), and VPShadeBlock(). |
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