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Merge pull request #6 from Medical-Image-Analysis-Laboratory/FaBiANv2…
….0-dev ENH: implement local white matter heterogeneities
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,53 @@ | ||
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
| % Function that redefines the position of the slice slab that covers % | ||
| % the fetal brain volume based on the shift that is applied in the % | ||
| % slice thickness direction between the acquisition of two % | ||
| % low-resolution series in the same orientation (as it is done in % | ||
| % clinical routine in the case of two successive series acquired in the % | ||
| % same plane). % | ||
| % % | ||
| % Fetal_Brain_shift = FOV_shift(Fetal_Brain, shift, orientation); % | ||
| % % | ||
| % inputs: - Fetal_Brain: segmented high-resolution 3D volume of the % | ||
| % fetal brain % | ||
| % - shift: displacement (in voxels) of the slice slab in the % | ||
| % slice thickness direction % | ||
| % - orientation: strict acquisition plane (axial, coronal or % | ||
| % sagittal) % | ||
| % % | ||
| % output: - Fetal_Brain_shift: segmented high-resolution 3D volume of % | ||
| % the fetal brain after a shift in the % | ||
| % slice thickness direction % | ||
| % % | ||
| % % | ||
| % Hélène Lajous, 2021-08-23 % | ||
| % [email protected] % | ||
| % % | ||
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
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| function Fetal_Brain_shift = FOV_shift(Fetal_Brain, ... | ||
| shift, ... | ||
| orientation) | ||
|
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| % Input check | ||
| if nargin < 3 | ||
| error('Missing input(s).'); | ||
| elseif nargin > 3 | ||
| error('Too many inputs.'); | ||
| end | ||
|
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| % Resize the fetal brain volume to allow shifting in any direction | ||
| Fetal_Brain_FOV = {1+ceil(abs(shift)):size(Fetal_Brain,1)-ceil(abs(shift)); 1+ceil(abs(shift)):size(Fetal_Brain,2)-ceil(abs(shift)); 1+ceil(abs(shift)):size(Fetal_Brain,3)-ceil(abs(shift))}; | ||
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| % Slightly shift the slice slab in the slice thickness direction (as done | ||
| % in the clinics) | ||
| Fetal_Brain_FOV{orientation} = Fetal_Brain_FOV{orientation} + shift; | ||
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| % Mask the fetal brain after having shifted the slice slab | ||
| Fetal_Brain_shift = Fetal_Brain(Fetal_Brain_FOV{1}, Fetal_Brain_FOV{2}, Fetal_Brain_FOV{3}); | ||
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| % Display message for debugging | ||
| sprintf('The fetal brain volume has been shifted by %d voxels in the slice thickness direction.', shift) | ||
|
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||
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
| % Function that redefines the position of the slice slab that covers % | ||
| % the fetal brain volume based on the shift that is applied in the % | ||
| % slice thickness direction between the acquisition of two % | ||
| % low-resolution series in the same orientation (as it is done in % | ||
| % clinical routine in the case of two successive series acquired in the % | ||
| % same plane). % | ||
| % % | ||
| % Fetal_Brain_shift = FOV_shift(Fetal_Brain, shift, orientation); % | ||
| % % | ||
| % inputs: - Fetal_Brain: segmented high-resolution 3D volume of the % | ||
| % fetal brain % | ||
| % - shift: displacement (in voxels) of the slice slab in the % | ||
| % slice thickness direction % | ||
| % - orientation: strict acquisition plane (axial, coronal or % | ||
| % sagittal) % | ||
| % % | ||
| % output: - Fetal_Brain_shift: segmented high-resolution 3D volume of % | ||
| % the fetal brain after a shift in the % | ||
| % slice thickness direction % | ||
| % % | ||
| % % | ||
| % Hélène Lajous, 2021-08-23 % | ||
| % [email protected] % | ||
| % % | ||
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
|
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||
|
|
||
| function Fetal_Brain_shift = FOV_shift(Fetal_Brain, ... | ||
| shift, ... | ||
| orientation) | ||
|
|
||
| % Input check | ||
| if nargin < 3 | ||
| error('Missing input(s).'); | ||
| elseif nargin > 3 | ||
| error('Too many inputs.'); | ||
| end | ||
|
|
||
| % Resize the fetal brain volume to allow shifting in any direction | ||
| Fetal_Brain_FOV = {1+ceil(abs(shift)):size(Fetal_Brain,1)-ceil(abs(shift)); 1+ceil(abs(shift)):size(Fetal_Brain,2)-ceil(abs(shift)); 1+ceil(abs(shift)):size(Fetal_Brain,3)-ceil(abs(shift))}; | ||
|
|
||
| % Slightly shift the slice slab in the slice thickness direction (as done | ||
| % in the clinics) | ||
| Fetal_Brain_FOV{orientation} = Fetal_Brain_FOV{orientation} + shift; | ||
|
|
||
| % Mask the fetal brain after having shifted the slice slab | ||
| Fetal_Brain_shift = Fetal_Brain(Fetal_Brain_FOV{1}, Fetal_Brain_FOV{2}, Fetal_Brain_FOV{3}); | ||
|
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||
| % Display message for debugging | ||
| sprintf('The fetal brain volume has been shifted by %d voxels in the slice thickness direction.', shift) | ||
|
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||
| end |
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