Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add merge ROIs feature #9

Draft
wants to merge 6 commits into
base: main
Choose a base branch
from
Draft

add merge ROIs feature #9

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions src/roi/createRoi.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,29 @@

mask = createRoiLabel(mask);

case 'merge'

roiImages = specification;
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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. :-)

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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')};

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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');


mask = [];

% loop through the ROIs to merge
for iRoi = 1:length(roiImages)

% load one ROI per time
maskToMerge = spm_read_vols(spm_vol(roiImages{iRoi}));

mask = cat(4, mask, maskToMerge);

end

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

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

case 'expand'

% Ugly hack
Expand Down