Extract subset of time-curves from a 4D volume

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Domenico
Domenico 2020-6-10
评论： Turlough Hughes 2020-6-17
Dear all,
I have a 4D volume and I can easily extract the temporal curve for each voxel.
I would like to extract only the curves for the voxels that correspond to a certain condition.
For example: V is the 4D volume and R is a 3D mask volume. I would like to extract only the curves of the points in which R>0 but without using a for cicle.
Normally I would write:
for k=1:size(V,3)
for i=1:size(V,1)
for j =1:size(V,2)
if (R(i,j,k)>0)
y = squeeze(V(i,j,k,:));
a(i,:) = y;
......
end
end
end
I tried to use indexing but I can only use it with 3D volumes.
Is there an efficient solution (I mean fast) to do this?
Thanks a lot
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Turlough Hughes
Turlough Hughes 2020-6-10
You could do something like this.
V2 = V; % make a copy of V
V2(repmat(R<=0,1,1,1,size(V2,4)))=NaN; % Remove values where R <= 0
My feeling is that you should maintain the shape of V, so I opted to insert NaN's at coordinates where your condition R>0 is false, ie where R<=0 is true. Is that the sort of answer you're looking for?
Domenico
Domenico 2020-6-10
Thanks a lot.
In this way you obtain a sort of "masking" of the 4D volume, right? From that masking, however, I would like to extract each single temporal 1D curve, i.e. for every survived pixel I would like to obtain its curve (without using for)

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Turlough Hughes
Turlough Hughes 2020-6-17
I can reduce this to a single for loop which iterates through the timesteps but i'm not sure about doing this entirely without loop. Here, I concatentate the data of a given timestep into a column vector and insert it into results. I took the liberty of including the x,y and z indices in columns 1,2 and 3, respectively, so each timestep is added sequentially thereafter.
Rmask = R>0; % Binary mask
[Ix, Iy, Iz] = ind2sub(size(Rmask),find(Rmask)); % get x,y,z indices for mask
result = [Ix, Iy, Iz, zeros(numel(Ix),size(V,4))]; % preallocate space
for t = 1:size(V,4)
Vtemp = V(:,:,:,t); % grab one timestep
result(:,t+3) = Vtemp(Rmask); % Convert to column vector and insert into results
end
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Domenico
Domenico 2020-6-17
Ok, only a question: what do you do with Ixyz? You obtain it but you don't use it for Vr. Is right?
Turlough Hughes
Turlough Hughes 2020-6-17
Ixyz is the corresponding index in V. The first row of Vr shows values changing over time at a single point within V, the first row of Ixyz inidicates the corresponding xyz indices within V which can usually be related to an xyz position. I just assumed you would need it.

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