Matlab Code for Reducing FA: Difference between revisions

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Return to [[Christine McLeavey & Jessica Tsang]]
Return to [[2009 Christine McLeavey & Jessica Tsang]]
<br>
<text>
<br>function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize)
function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize)
<br>
<br>% input:
<br>%  dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat'))
<br>%  mask: name of brain mask, ie 'ab_mask.nii.gz'
<br>%  densitymap: image of fiber density (betw 0 and 1), i.e. using
<br>%      dtiComputeFiberDensityNOGUI
<br>%  effectsize: the factor by which to lower/raise FA (to be weighted by
<br>%      fiber density). With effectsize of 0.1, weighted effectsize =
<br>%      0.1*fiberdensity, and newFA = origFA*[1-(weighted effectsize)]
<br>%
<br>% returns:
<br>%  XxYxZ image with altered fa, in image space
<br>%
<br>% 2009.11.15 JT
<br>
<br>fa = dtiComputeFA(dt6);
<br>brainMask=readFileNifti(mask);
<br>brainMask.data=double(brainMask.data);
<br>% effectsize = .1;


<br>weightedESmap = effectsize*densitymap;
% input:
<br>alteredFA = fa.*(1-weightedESmap);
%  dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat'))
<br>alteredFAmasked = alteredFA.*brainMask.data;
%  mask: name of brain mask, ie 'ab_mask.nii.gz'
<br>
%  densitymap: image of fiber density (betw 0 and 1), i.e. using
<br>% fa = dtiComputeFA(dt6);
%      dtiComputeFiberDensityNOGUI
<br>% weightedESmap = effectsize*densitymap;
%  effectsize: the factor by which to lower/raise FA (to be weighted by
<br>% alteredFA = fa.*(1-weightedESmap);
%      fiber density). With effectsize of 0.1, weighted effectsize =
<br>
%      0.1*fiberdensity, and newFA = origFA*[1-(weighted effectsize)]
<br>return
%
% returns:
%  XxYxZ image with altered fa, in image space
%
% 2009.11.15 JT
 
fa = dtiComputeFA(dt6);
brainMask=readFileNifti(mask);
brainMask.data=double(brainMask.data);
% effectsize = .1;
 
weightedESmap = effectsize*densitymap;
alteredFA = fa.*(1-weightedESmap);
alteredFAmasked = alteredFA.*brainMask.data;
 
% fa = dtiComputeFA(dt6);
% weightedESmap = effectsize*densitymap;
% alteredFA = fa.*(1-weightedESmap);
 
return<text>

Revision as of 20:37, 9 December 2009

Return to 2009 Christine McLeavey & Jessica Tsang <text> function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize)

% input: % dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat')) % mask: name of brain mask, ie 'ab_mask.nii.gz' % densitymap: image of fiber density (betw 0 and 1), i.e. using % dtiComputeFiberDensityNOGUI % effectsize: the factor by which to lower/raise FA (to be weighted by % fiber density). With effectsize of 0.1, weighted effectsize = % 0.1*fiberdensity, and newFA = origFA*[1-(weighted effectsize)] % % returns: % XxYxZ image with altered fa, in image space % % 2009.11.15 JT

fa = dtiComputeFA(dt6); brainMask=readFileNifti(mask); brainMask.data=double(brainMask.data); % effectsize = .1;

weightedESmap = effectsize*densitymap; alteredFA = fa.*(1-weightedESmap); alteredFAmasked = alteredFA.*brainMask.data;

% fa = dtiComputeFA(dt6); % weightedESmap = effectsize*densitymap; % alteredFA = fa.*(1-weightedESmap);

return<text>

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