signal intensity value in MRI dicom file

Can Anybody help me to extract matlab code to extract signal intensity value in MRI dicom file with the corresponding pixel coordination? here i have attached dicom file Brain http://www.osirix-viewer.com/datasets/DATA/BRAINIX.zip

Answer 1

[harjeet singh]

hello Ranga use this to exract signal intensity

X = uint8(dicomread('IM-0001-0001'));
figure(1)
imshow(X)

pixel_co=[256 200];
pixel_vale=X(pixel_co(1),pixel_co(2))

[Walter Roberson]

Caution: in general, dicom files often have intensities outside the range 0 to 255. Depending on the modality, values up to about 1790 are common, and some modalities use negative values as well. Some of the modalities commonly use floating point values.

[Ranga Tudugala]

Dear Harjeet Singh

Its gives 0 every time..

can you explain pixel_co=[256 200]; what does it do?

i need to get pixel coordination and its actual Signal Intensity ( pixel value i can get from directly from X variable know isnt it ?)

[harjeet singh]

pixe_co is the variable having position of which intensity you want from the image

[Image Analyst]

pixel_co is an array with the pixel location in the form [row, column], so 256 is the row and 200 is the column. But we need to know what "the corresponding pixel coordination" means. Coordination means like the opposite of clumsy, or a series of activities in harmony with someone or something else, like "harjeet and I are working in coordination to solve your question." Do you really mean "coordinates"?

[Walter Roberson]

If you get 0 every time then your data might have been negative and you should probably not have converted to uint8... as I cautioned could be a problem. Remove the uint8() part and try again and see what the values are.

[Image Analyst]

If you remove uint8() and find that it is negative, you will probably have to use [] in imshow():

imshow(X, []);

Answer 2

[Image Analyst]

Try calling impixelinfo() to interactively view the value as you mouse around over the image.

grayImage = dicomread(fullFileName);
imshow(grayImage);
colorbar;
hp = impixelinfo();

Or you can call imtool().

Answer 3

[Ranga Tudugala]

Okay Thanks...Guys..

I have extracted pixel value which I needed but now im struggling. I need to select every pixel which having particular value (range) in the image. any body ?

[Walter Roberson]

mask = YourArray >= low_value & YourArray <= high_value;
selected_pixels = YourArray(mask);

[Ranga Tudugala]

Thanks Its works

But not in the way I need, it should be show in the Image.. not as vector Mx

[Walter Roberson]

mask = YourArray >= low_value & YourArray <= high_value;
NewImage = YourArray .* mask;
imshow(NewImage);

[Ranga Tudugala]

(Y) Great.... Your Array.* Int16(mask) ;

It WORKED

Well Im working on converting CT image to MR Image... did you try such stupid thing ?

[Image Analyst]

Of course you can't turn an x-ray image into a magnetic image (I assume you know that). So, do you mean aligning them -- or "multimodality registration"?

By the way, an alternate way of masking is this:

NewImage = YourArray; % Initialize
NewImage(~mask) = 0; % Set outside mask to 0

I use both at various times. I've never timed them to see which (multiplication or assignment) is faster because they're both really fast.

[Ranga Tudugala]

Articulacy It CAN.. that the researchers Do... what they seems cnt.. I think you are genius than me. you can do it easily.. I think i have found the best resource person.. for that..

here I hv attached the paper "MRI-based treatment planning with pseudo CT generated through atlas registration." http://www.ncbi.nlm.nih.gov/pubmed/24784377

[Image Analyst]

Well Star could answer better than me, but I'm reading "A pseudo CT...[snip]...was generated by deforming atlas CT images...[snip]. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images"

So it sounds like they're aligning/warping CT images with the formula for warping based on MRI images, or what I called multi-modality registration. Maybe that's what you meant. I was thinking that you wanted to take MRI images and convert them to have it look just as if you'd taken a CT of the patient instead of an MRI. I think you can align CT or MRI volumes in a variety of ways, but I don't think you can get one from the other. Otherwise hospitals would not have two separate multi-million dollar instruments when they could get by with one.

Star, what do you think?

Answer 4

[Ranga Tudugala]

wneh im run this tutorial http://in.mathworks.com/help/images/registering-multimodal-mri-images.html#zmw57dd0e13337

Im getting this error after this codes

movingRegisteredAffineWithIC = imregister(moving,fixed,'affine',optimizer,metric,...
    'InitialTransformation',tformSimilarity);

This is the error

Error using imregtform>parseInputs (line 240)
Parameters must be a character.

Error in imregtform (line 119)
parsedInputs = parseInputs(varargin{:});

Error in imregister (line 115)
tform = imregtform(varargin{:});

can somebody tell what happened ?

[Walter Roberson]

Please start a new Question for this.