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[ENH] improve roi plotting #46

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Merged
merged 3 commits into from
Jun 5, 2022
Merged

[ENH] improve roi plotting #46

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734776b
add possibility to add description to roi plotting
Remi-Gau Jun 5, 2022
cfe72dc
make resliceRoiImage more flexible
Remi-Gau Jun 5, 2022
becc14f
fix default output
Remi-Gau Jun 5, 2022
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6 changes: 5 additions & 1 deletion src/roi/plotDataInRoi.m
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Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,11 @@ function labelAxis(roiAs, rows, cols, subplotList, roiImages, dataLabel)
subplot(rows, cols, subplotList(1, i));

bf = bids.File(roiImages{i});
title(sprintf('roi: %s', bf.entities.label));
desc = '';
if isfield(bf.entities, 'desc')
desc = sprintf('- desc: %s', bf.entities.desc);
end
title(sprintf('roi: %s%s', bf.entities.label, desc));

subplot(rows, cols, subplotList(end, i));

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33 changes: 28 additions & 5 deletions src/roi/resliceRoiImages.m
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Original file line number Diff line number Diff line change
@@ -1,10 +1,31 @@
% (C) Copyright 2021 CPP ROI developers

function reslicedImages = resliceRoiImages(referenceImage, imagesToCheck)
function [reslicedImages, matlabbatch] = resliceRoiImages(referenceImage, imagesToCheck, dryRun)
%
% Check if images are in the same orientation and reslice if necessarrry.
%
% USAGE::
%
% reslicedImages = resliceRoiImages(referenceImage, imagesToCheck, dryRun)
%
% :param referenceImage:
% :type referenceImage: path
%
% :param imagesToCheck:
% :type imagesToCheck: path or cellstr
%
% :param dryRun: Returns the matlabbatch without running it.
% :type dryRun: logical
%
% (C) Copyright 2021 CPP ROI developers

% TODO
% - allow option to binarize output?

if nargin < 3
dryRun = false;
end

matlabbatch = {};

% check if files are in the same space
% if not we reslice the ROI to have the same resolution as the data image
sts = checkRoiOrientation(referenceImage, imagesToCheck);
Expand All @@ -13,9 +34,11 @@

else

matlabbatch = {};
matlabbatch = setBatchReslice(matlabbatch, referenceImage, imagesToCheck);
spm_jobman('run', matlabbatch);

if ~dryRun
spm_jobman('run', matlabbatch);
end

basename = spm_file(imagesToCheck, 'basename');
reslicedImages = spm_file(imagesToCheck, 'basename', ...
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