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add merge ROIs feature #9

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add merge ROIs feature #9

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41f57eb
add merge case in createRoi
marcobarilari Mar 31, 2021
f64faa0
add code to load ROIs to merge
marcobarilari Mar 31, 2021
1ddb0bf
clean and add code to sum the rois
marcobarilari Mar 31, 2021
97b6e30
add some comments
marcobarilari Mar 31, 2021
5d4e9c2
add check that there are no >1 values after sum
marcobarilari Mar 31, 2021
d7af28b
simplify how to load the masks and merge them
marcobarilari Apr 1, 2021
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27 changes: 27 additions & 0 deletions src/roi/createRoi.m
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,33 @@

mask = createRoiLabel(mask);

case 'merge'

roiImages = specification;
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We are still developping this but I suspect we'll want to have the same way to use specification for all "cases":

so that it will be something like :

specification(1).mask = roi_filenameA
specification(2).mask = roi_filenameB

not necessary to have now but just to let you know that the "API" and the type and name of arguments for this function are still a moving target. :-)

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not sure if this replys to it but in a batch file you would have eg

roiImages = {fullfile(opt.ROI.roiDir, 'label-sphere5xMinus40yMinus50zMinus22_mask.nii'); ...
             fullfile(opt.ROI.roiDir, 'label-sphere5x36yMinus46zMinus17_mask.nii')};

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More like this

specification(1).mask = fullfile(opt.ROI.roiDir, 'label-sphere5xMinus40yMinus50zMinus22_mask.nii');
specification(2).mask = fullfile(opt.ROI.roiDir, 'label-sphere5x36yMinus46zMinus17_mask.nii');


% loop through the ROIs to merge
for iRoi = 1:length(roiImages)
% load one ROI per time
maskToMerge = load_untouch_nii(roiImages{iRoi});
% take the first ROI as reference to add the others to it
if iRoi == 1
mask = maskToMerge;
% delete the fileprefix argument to be re-assigned with the new one
mask.fileprefix = [];
else
% sum up the ROI masks
mask.img = mask.img + maskToMerge.img;
end

end

% check that there are no >1s
mask.img(mask.img > 1) = 1;
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I am pretty sure that in this case you can just convert mask.img to a logical array:

mask.img = logical(mask.img);

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I think that using

      % merge the logical masks into one
      mask = any(mask, 4);

will save us from having values >1

although, maybe for the future, we would like to have different values for each single single ROI merged

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If you mean having a single image that combines different masks has a different "label" for each ROI: I agree but I would have that as an entirely different function.
And I think that MarsBar must have some functions to do that.


% assign fileprefix (name to be save?)
% [ WIP ]
mask = createRoiLabel(mask);

case 'expand'

% Ugly hack
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