Matlab Code for Reducing FA - Revision history

imported>Psych 204 at 17:59, 11 December 2009

2009-12-11T17:59:42Z

@@ Line 3: / Line 3: @@
 <br>function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize)
 <br>
 <br>% input:
 <br>%   dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat'))
@@ Line 16: / Line 27: @@
 <br>%
 <br>% 2009.11.15 JT
 <br>% effectsize = .1;
 <br>% fa = dtiComputeFA(dt6);
 <br>% weightedESmap = effectsize*densitymap;

imported>Psych 204 at 20:39, 9 December 2009

2009-12-09T20:39:13Z

← Older revision		Revision as of 20:39, 9 December 2009
Line 30:		Line 30:
	<br>% alteredFA = fa.*(1-weightedESmap);		<br>% alteredFA = fa.*(1-weightedESmap);
	<br>		<br>
	<br>return~~<text>~~		<br>return

imported>Psych 204 at 20:38, 9 December 2009

2009-12-09T20:38:56Z

← Older revision		Revision as of 20:38, 9 December 2009
Line 1:		Line 1:
	Return to [[2009 Christine McLeavey & Jessica Tsang]]		Return to [[2009 Christine McLeavey & Jessica Tsang]]
	<~~text~~>		<br>
	function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize)		<br>function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize)
			<br>
	% input:		<br>% input:
	% dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat'))		<br>% dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat'))
	% mask: name of brain mask, ie 'ab_mask.nii.gz'		<br>% mask: name of brain mask, ie 'ab_mask.nii.gz'
	% densitymap: image of fiber density (betw 0 and 1), i.e. using		<br>% densitymap: image of fiber density (betw 0 and 1), i.e. using
	% dtiComputeFiberDensityNOGUI		<br>% dtiComputeFiberDensityNOGUI
	% effectsize: the factor by which to lower/raise FA (to be weighted by		<br>% effectsize: the factor by which to lower/raise FA (to be weighted by
	% fiber density). With effectsize of 0.1, weighted effectsize =		<br>% fiber density). With effectsize of 0.1, weighted effectsize =
	% 0.1fiberdensity, and newFA = origFA[1-(weighted effectsize)]		<br>% 0.1fiberdensity, and newFA = origFA[1-(weighted effectsize)]
	%		<br>%
	% returns:		<br>% returns:
	% XxYxZ image with altered fa, in image space		<br>% XxYxZ image with altered fa, in image space
	%		<br>%
	% 2009.11.15 JT		<br>% 2009.11.15 JT
			<br>
	fa = dtiComputeFA(dt6);		<br>fa = dtiComputeFA(dt6);
	brainMask=readFileNifti(mask);		<br>brainMask=readFileNifti(mask);
	brainMask.data=double(brainMask.data);		<br>brainMask.data=double(brainMask.data);
	% effectsize = .1;		<br>% effectsize = .1;
			<br>
	weightedESmap = effectsize*densitymap;		<br>weightedESmap = effectsize*densitymap;
	alteredFA = fa.*(1-weightedESmap);		<br>alteredFA = fa.*(1-weightedESmap);
	alteredFAmasked = alteredFA.*brainMask.data;		<br>alteredFAmasked = alteredFA.*brainMask.data;
			<br>
	% fa = dtiComputeFA(dt6);		<br>% fa = dtiComputeFA(dt6);
	% weightedESmap = effectsize*densitymap;		<br>% weightedESmap = effectsize*densitymap;
	% alteredFA = fa.*(1-weightedESmap);		<br>% alteredFA = fa.*(1-weightedESmap);
			<br>
	return<text>		<br>return<text>

imported>Psych 204 at 20:37, 9 December 2009

2009-12-09T20:37:35Z

@@ Line 1: / Line 1: @@
-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>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

imported>Psych 204 at 20:36, 9 December 2009

2009-12-09T20:36:58Z

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

imported>Psych 204: Created page with 'Return to function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize) % input: % dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat')) % mask: name of brain mask, ie …'

2009-12-09T20:32:59Z

Created page with 'Return to function alteredFAmasked = AlterFA(dt6, mask, densitymap, effectsize) % input: % dt6: ie dt.dt6 (can use dt=dtiLoadDt6('dt6.mat')) % mask: name of brain mask, ie …'

New page

Return to
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