Can we extract ROI of MRI images automatically?

Hi every one, I have a set of dicom files and I am trying to extract ROI of approximate region of knee cartilage automatically? I don't need the whole image, because the size of voxels is big. I want to extract an approximate small area around the tibiofemoral joint (knee joints). Does anyone know how can I do ROI extraction automatically? Or is there any commands to crop a rectangular part of image as ROI automatically?Is there any function that can automatically do that ? Your help is appreciated.

Answer 1

[Image Analyst]

You might try the grayconnected() function, but I think that that ROI might be connected to a bunch of other pixels that you don't want. You could perhaps try to repair it afterwards with activecontour(), but no guarantees. Alternatively freehand tracing is probably your best option. I'm attaching demos for that.

[Sara Salimi]

Dear Image Analyst,

Many Thanks for your help.

I really appreciate your help.

Regards Sara

Answer 2

[Walter Roberson]

If you knew the ROI location in the image then you could imcrop() passing in the bounding box. Or simply index into the image array.

If you do not know the exact location then the difficulty is going to depend upon how difficult it is to recognize the appropriate area. We would find it easier to advise you on that if you were to post a few different images -- at least two different patients, and if the MRI is taken at different Z coordinates then at least two different Z for one of the patients.

[Sara Salimi]

Dear Walter,

Many thanks for your reply. I have two sets of images; ROI has been extracted by expert (I attached two images) in one set. The other set is with out ROI that I am going to use as test set for classifier; however, I do need the whole area of image. Now, I want to crop approximate area of ROI. Because, the size of training set increase and there is imbalance number of voxels of ROI compared to other area and this can lead classifier to bias to the class with more number of samples (voxels). My next question is, is there any way(or command) to label voxels inside of ROI as one class and outside of ROI as another class(background)? I want to add a column (as class) to voxels' information which indicates the voxel class (class1/class0).

Hopefully, you know the answer :)

I really appreciate your help.

[Walter Roberson]

I think it is going to be tricky to get that ROI.

Once you have an ROI, you can use roi2mask and then use the mask to set values (and use the logical negation to set the other value). For example,

imgclass = zeros(size(TheROI), 'uint8');
rmask = roi2mask(TheROI);
imgclass(rmask) = 1;   %foreground
imgclass(~rmask) = 0;  %background

However in the particular case of those two values, you could use

rmask = roi2mask(TheROI);
imgclass = uint8(rmask);

as the mask is going to be logical 1 where the ROI is and logical 0 elsewhere. The uint8() part can be omitted if you are not planning to store values other than 0 and 1 there.

[Sara Salimi]

Dear Walter,

Many thanks for your help.

I really appreciate your help.

Regards

Sara