MATLAB: Issue with writing DICOM images to a folder (‘Could not open folder for writing’ error)

dicomdicomwriteimage analysisimage processingImage Processing Toolboximage segmentation

I have a script to apply a manual segmentation to a set of DICOM images in a for loop. I want to write the segmentation for each image to a specific (initially empty) folder.

baseFileName = sprintf('%s_%d.dcm', cnt); 
fullFileName = fullfile(pwd, 'Project_Segmentations', baseFileName); 
dicomwrite(segmentation, fullFileName);

The error message I'm getting is:

Error using dicom_open_msg (line 31)
Could not open "Project\DICOMs_Project\_" for writing
Error in dicomwrite>write_stream (line 660)
file = dicom_open_msg(file, 'w');
Error in dicomwrite>encodeAndWriteAttrs (line 325)
msg = write_stream(destination, data_stream);
Error in dicomwrite>write_message (line 282)
    encodeAndWriteAttrs(attrs, options, filename, specificCharacterSet);
Error in dicomwrite (line 208)
    [status, options] = write_message(X, filename, map, metadata, options);
Error in ManualSegmentationFull (line 80)
dicomwrite(segmentation, fullFileName);

Thanks in advance for any advice you may have!

Best Answer

The problem seemed to be down to trying to use, I think it must have been creating an invalid file name:

'%s_%d.dcm'

This code actually works fine, writing to the correct folder, when I simply use:

baseFileName = sprintf('Segmentation_%d.dcm', cnt);
fullFileName = fullfile(pwd, 'Project_Segmentations',baseFileName); 
% Write the DICOM segmentation to the folder. 
dicomwrite(segmentation, fullFileName);

What I actually want is for the DICOMs to be written with the file name format of 'OrginalFileName_Segmentation.dcm'. If anyone can advise me on this it'd be really helpful, but for now the file name format I'm using is acceptable for my application.

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MATLAB: How to solve the error

 Could not open "rice.dcm" for writing

This can mean, that the file is write-protected or you do not have the permissions to write in this folder. Check this either in the file explorer of the operating system or by the fileattrib command.

This tries to create the file in the current folder:

dicomwrite(I,'rice.dcm',info)

Better define the folder to write to explicitly. fullfile might be useful here.

MATLAB: Finding tortuosity of parasite

Use bwskel() to get the longest spine. Then use bwmorph() to get the endpoints of the spine. Then use find() and sqrt() to get the straight line distance between the endpoints, then divide the two.

% This demo computes the tortuosity of a snake-like shape by dividing the actual longest spine distance by the straight line distance between the endpoints.
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 15;
%--------------------------------------------------------------------------------------------------------

%    READ IN IMAGE
folder = pwd;
baseFileName = 'worm.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
	% The file doesn't exist -- didn't find it there in that folder.
	% Check the entire search path (other folders) for the file by stripping off the folder.
	fullFileNameOnSearchPath = baseFileName; % No path this time.
	if ~exist(fullFileNameOnSearchPath, 'file')
		% Still didn't find it.  Alert user.
		errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
		uiwait(warndlg(errorMessage));
		return;
	end
end
% Read in the image from disk.  If storedColorMap is not empty, it's an indexed image with a stored colormap.
[grayImage, storedColorMap] = imread(fullFileName);
if ~isempty(storedColorMap)
	grayImage = ind2rgb(grayImage, storedColorMap);
end
% Get the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
	% It's not really gray scale like we expected - it's color.
	% Use weighted sum of ALL channels to create a gray scale image.
	grayImage = rgb2gray(grayImage);
	% ALTERNATE METHOD: Convert it to gray scale by taking only the green channel,
	% which in a typical snapshot will be the least noisy channel.
	% grayImage = grayImage(:, :, 2); % Take green channel.
end
% Display the image.
hFig = figure;
subplot(1, 2, 1);
imshow(grayImage, []);
title('Original Grayscale Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;
%--------------------------------------------------------------------------------------------------------
%    SEGMENTATION
% Binarize the image
binaryImage = imbinarize(grayImage);
% Take the largest blob only.
binaryImage = bwareafilt(binaryImage, 1);
% Fill holes, if any.
binaryImage = imfill(binaryImage, 'holes');
% Display the binary image.
subplot(1, 2, 1);
imshow(binaryImage, []);
title('Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
% Now skeletonize
skelImage = bwskel(binaryImage); % First guess.  Will have short spurs.
% First get the area of the skeleton and take half of it to be the longest spine length.
% This will get rid of all spurs.
MinBranchLength = round(sum(skelImage(:))/2)
% Now take the skeleton again using that min branch length we just computed.
skelImage = bwskel(binaryImage, 'MinBranchLength', MinBranchLength);
% Display the skeleton image.
subplot(1, 2, 2);
imshow(skelImage, []);
title('Skeleton Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
% Find the endpoints
endpointImage = bwmorph(skelImage, 'endpoints');
[rows, columns] = find(endpointImage)
% Draw a red line between them.
hold on;
plot(columns, rows, 'r-', 'LineWidth', 2);
% Find the spine length.
% (Would be more accurate to find the spine length by traversing it.)
spineLength = sum(skelImage(:))
% Compute the straight line distance.
straightLineDistance = sqrt((columns(2) - columns(1))^2 + (rows(2) - rows(1))^2)
% Compute the tortuosity
tortuosity = spineLength / straightLineDistance
caption = sprintf('Skeleton Image.  Tortuosity = %f', tortuosity);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');

Best Answer

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