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Fix deprecated avifile/addframe API and timeseries_extract_slice returning all zeros #70

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Fix deprecated avifile/addframe API and timeseries_extract_slice returning all zeros #70

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Initial plan
Copilot Mar 9, 2026
babb377
Fix deprecated avifile/addframe and all-zeros timeseries_extract_slice
Copilot Mar 9, 2026
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64 changes: 37 additions & 27 deletions CanlabCore/Data_extraction/timeseries_extract_slice.m
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Original file line number Diff line number Diff line change
Expand Up @@ -6,28 +6,25 @@
% :Usage:
% ::
%
% function sl = timeseries_extract_slice(V,sliceno)
% function sl = timeseries_extract_slice(V, sliceno, orientation)
%
% :Inputs:
%
% **V:**
% image filenames (char) or spm_vol memory-mapped volumes
%
% **sliceno:**
% slice number (voxel index) to extract
%
% **orientation:**
% 'axial' (default), 'sagittal', or 'coronal'
%
% :Output:
%
% **sl:**
% X x Y x time matrix of slice data
%

global defaults

% defaults
switch spm('Ver')
case 'SPM2'
% spm_defaults is a script
disp('WARNING: spm defaults not set for spm2. Make sure your defaults are set correctly');

case {'SPM5', 'SPM8', 'SPM12'}
% spm_defaults is a function
spm_defaults()

otherwise
% unknown SPM
disp('Unknown version of SPM!');
spm_defaults()
end


if ischar(V)
V = spm_vol(V);
end
Expand All @@ -38,16 +35,29 @@

switch(orientation)
case 'axial'
get_slice = @get_ax_slice;
% Map output pixel (x,y) -> voxel (x, y, sliceno)
mat = spm_matrix([0 0 sliceno]);
for i = 1:length(V)
sl(:,:,i) = spm_slice_vol(V(i), mat, V(i).dim(1:2), 0);
end

case 'sagittal'
get_slice = @get_sag_slice;
% Map output pixel (x,y) -> voxel (sliceno, x, y)
% Matrix maps: x_vox=sliceno (const), y_vox=x_pix, z_vox=y_pix
mat = [0 0 0 sliceno; 1 0 0 0; 0 1 0 0; 0 0 0 1];
for i = 1:length(V)
sl(:,:,i) = spm_slice_vol(V(i), mat, V(i).dim(2:3), 0);
end

case 'coronal'
get_slice = @get_cor_slice;
% Map output pixel (x,y) -> voxel (x, sliceno, y)
% Matrix maps: x_vox=x_pix, y_vox=sliceno (const), z_vox=y_pix
mat = [1 0 0 0; 0 0 0 sliceno; 0 1 0 0; 0 0 0 1];
for i = 1:length(V)
sl(:,:,i) = spm_slice_vol(V(i), mat, [V(i).dim(1) V(i).dim(3)], 0);
end

otherwise
error('Unknown orientation: %s\n', orientation);
end

for i = 1:length(V)
sl(:,:,i) = get_slice(V(i), sliceno);
end
end
8 changes: 6 additions & 2 deletions CanlabCore/Visualization_functions/Support/movie_tools.m
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Original file line number Diff line number Diff line change
Expand Up @@ -393,7 +393,10 @@
switch(FRAMESTYLE)
case 'avi' % write to avi format directly
if isempty(mov)
mov = avifile('mymovie.avi','Quality',75,'Compression','None','Fps',fps);
mov = VideoWriter('mymovie.avi');
mov.Quality = 75;
mov.FrameRate = fps;
open(mov);
end

case 'matlab' % matlab movie format
Expand Down Expand Up @@ -425,7 +428,8 @@
drawnow

try
mov = addframe(mov,H);
frame = getframe(H);
writeVideo(mov, frame);
catch
disp('Cannot write frame. Failed to set stream format??')
mov = close(mov);
Expand Down
8 changes: 5 additions & 3 deletions CanlabCore/Visualization_functions/movie_of_slice_timeseries.m
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,8 @@ function movie_of_slice_timeseries(imgs, slicenumber, moviename, orientation)
title(sprintf('Image %3.0f: %s', i, ff), 'FontSize', 24)

% mov = add_a_frame(mov, H);
writeVideo(mov, H);
frame = getframe(H);
writeVideo(mov, frame);
end

tmp = close(mov); %#ok;
Expand All @@ -77,7 +78,7 @@ function movie_of_slice_timeseries(imgs, slicenumber, moviename, orientation)

% frame_rate = 1/tr;
mov = VideoWriter(moviename);
mov.Quality
mov.Quality = 75;
mov.FrameRate = fps;
open(mov);

Expand All @@ -96,7 +97,8 @@ function movie_of_slice_timeseries(imgs, slicenumber, moviename, orientation)

lightRestoreSingle(H);
try
mov = addframe(mov, H);
frame = getframe(H);
writeVideo(mov, frame);
catch
disp('Cannot write frame. Failed to set stream format??')
mov = close(mov);
Expand Down
10 changes: 2 additions & 8 deletions CanlabCore/hewma_utility/get_ax_slice.m
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Original file line number Diff line number Diff line change
Expand Up @@ -39,16 +39,10 @@

% Transverse slice
%==========================================================
C = [1 0 0 0;0 1 0 0;0 0 1 0;0 0 0 1];
DIM = V(1).dim(1:2);
mat = spm_matrix([0 0 slice_num]);

C(3,4) = slice_num;
%C(3,4)=-p;

% img = rot90(spm_slice_vol(V,C,DIM,0));
% img = spm_slice_vol(V,inv(C),DIM,0);
for i=1:length(V)
slice_data(:,:,i) = spm_slice_vol(V(i), C, DIM, 0);
slice_data(:,:,i) = spm_slice_vol(V(i), mat, V(i).dim(1:2), 0);
end

slice_data = squeeze(slice_data);
Expand Down