loading file from my directory?

Dear I would like to download imagej-nii and also ROI (from imageJ software) and calculate the mean and std of the voxels within adjacent 5 slices (3D volume) for 6 animals. I have created code but many errores I have,,,, cause I am so beginner to use matlab.

Sabjects={'animal1', 'animal2', 'animal3','animal4', 'animal5,'animal6'}; % for multi animal calculation.

for i =1: size(subjects,2); image = load - nii(['\MRI\..\'subjects(i)'\roi.nii']); for j = 0:1 region = voxel (mod = = i); deviation (j,i+1)= std (region,[],3); end end

%% this is for one animal image = load-nii ("name of the file"); roi = load-nii ("name of the file"); view-nii (roi); view-nii (image);

region1= voxels ((mod (roi ,2) == 1).* (roi > 0)); region2= voxels ((mod (roi ,2) == 0).* (roi > 0)); deviation = std (region ,[] ,3);

[David Young]

It will help people to answer if you format your question by indenting all lines of code, or highlighting it and clicking the "{} Code" button. Please edit your question - don't put the revised question into an answer.

[Image Analyst]

Please read this and format. http://www.mathworks.com/matlabcentral/answers/13205-tutorial-how-to-format-your-question-with-markup

Also, in what form is your ROI from ImageJ stored? Some kind of file???

[Dhafer]

< I would like to download imagej-nii and also ROI (from imageJ software) and calculate the mean and std of the voxels within adjacent 5 slices (3D volume) for 6 animals. I have created code but many errores I have,,,, cause I am so beginner to use matlab. >

< I do not know what is the ROI format, because it is appeaer as text. When I cearch on the ImageJ website, there is now specific format for the ROI. >

% for multi animal calculation.

      Sabjects={'animal1', 'animal2', 'animal3','animal4', 'animal5,'animal6'};   
      for i =1: size(subjects,2); 
      image = load - nii(['\MRI\..\'subjects(i)'\roi.nii']); 
      for j = 0:1 
      region = voxel (mod = = i); 
      deviation (j,i+1)= std (region,[],3); 
      end 
      end      

%%this is for one animal   

      image = load-nii ("name of the file"); 
      roi = load-nii ("name of the file");
      view-nii (roi); view-nii (image);    
      region1= voxels ((mod (roi ,2) == 1).* (roi > 0)); 
      region2= voxels ((mod (roi ,2) == 0).* (roi > 0)); 
      deviation = std (region ,[] ,3);

[Image Analyst]

Do not call variables "image" or "load" since those are the names of built in functions. Also == does NOT have a space between the equals. And what is load-nii? You can't have a function name with a minus sign in it. And, it's not clear what that function returns: an image or some kind of ROI coordinates. And what is "voxel"? Where is function view-nii? Again, you can' thvae a minus sign in the function name. Also, mod is a function so you can't do "mod = = 1". MATLAB is case sensitive so "Sabjects" and "subjects" are two different variables - I don't think that's what you intended. Finally, you can't have indexes of 0. They must start with 1.

Answer 1

[Mark Hayworth]

Perhaps this: http://www.mathworks.com/matlabcentral/fileexchange/32479-import-imagej-rois