Hi

You can not directly read the BRATS 2013 or 2014 directly into Matlab as the .mha format is not supported. To tackle this problem, first, I used to convert the .mha to . raw format. Second I read the .raw into Matlab using file manipulation functions (fopen, fread).

To summarize:

1- You can use the MITK visualization software to convert from .mha to .raw

2- Use the following Matlab toolbox to read the .raw

http://www.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3d

If you face any problem, you can write it down here.

Good Luck

Thank you Ahmad.

I have used the MATLAB toolbox to read .mha files. Now let me try the conversion you have asked.

Hello Ahmed, 

I worked on mitk software, but i do not find it may convert files from another.  I can only visualize them, but file has been saved in .mitk format. Please suggest me something how can I convert into a format which is supported by MATLAB.

Please refer to Ahmed's reply (who is my PhD student):

You can not directly read the BRATS 2013 or 2014 directly into Matlab as the .mha format is not supported. To tackle this problem, first, I used to convert the .mha to . raw format. Second I read the .raw into Matlab using file manipulation functions (fopen, fread).

To summarize:

1- You can use the MITK visualization software to convert from .mha to .raw

2- Use the following Matlab toolbox to read the .raw

http://www.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3

How can I access .mha (Medical) images in MATLAB? - ResearchGate. Available from: https://www.researchgate.net/post/How_can_I_access_mha_Medical_images_in_MATLAB [accessed Jan 21, 2016].

Thank you very much sir, I am trying to do that conversion.

To read the .mha 3D volume of data in Matlab, you can use the following code at this link:

http://in.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3d/content/mha/mha_read_volume.m

 Thank you all. I got the way to convert .mha images to .jpg format.

Converting .mha to .jpg will result in information loss. Better to convert it to .raw format and access it directly. If you are unable to convert using MITK software, you need to right-click on the file you want to convert from the "Data Manger" window in the upper left corner then choose "save" and select your desired format (check the attache file). It is so easy, then you can read the volume file into Matlab easily

Thank you very much Ahmed.

http://matlabimaging.blogspot.in/2016/02/medical-image-processing-1.html

@ Neha Baraiya How you have separated axial, coronal and sagital planes of 3D data?

you cannot read .mha files directly in matlab code. 

Please refer to my previous answers of this questions.

Good Luck

I have done operations on axial slices. 3d segmentation has not been done in my work

i am facing problem installing MITk Visualization software. i have downloaded the zip file and have no clue how to proceed further. kindly suggest something..http://mitk.org/wiki/Downloads#Getting_Started.

this is the link i have used

got it done..thank you all..

Done!! Thank you all.

you can use mipav to view the .mha file and you can also convert it to .jpg format. here is the link http://mipav.cit.nih.gov/clickwrap.php @Neha Baraiya ·

I am having problem in downloading BRATS2013 datasets.. can anybody help? My mail id is [email protected]. i just need few mri images and its ground truth. I want to analyize d segmentation method based on accuracy. And also trying to figure out few more parameters for comparision. Which all parameter can we use to judge the final detected tumors using segmentation? 

I have download BRATS2012 data sets.. if it is helpful for you then i can mail it.@ Shah Jinal 

@kanishka.. yeah sure.. send it.. :-) reply awaited..

V = mha_read_volume('.mha');

imshow(squeeze(V(:,:,round(end/2))),[]);

imshow(squeeze(V(:,:,125)),[]);

u can use this code,direct from the mha file

o.k. I will try this code and will let you know the response

I read the BRATS database as directed by you. But how to save our output in .mha format again. Thank you.

Although there are some ways to save the image file in . mha format, but it is  better save the output as metaimage (Header file with .mhd and Raw data file with .raw). 

Use the attached code to write the out put into metaimage format. 

Best of Luck

Thank you for your quick reply sir. If I wish to save in .mha format only then how can I do it? I am asking this because for BRATS online evaluation system we need to have our output file in .mha format only.

Dear,

        You can save the output image to . mhd using the above code then you can use MITK visualization toolkit to convert from .mhd to any desired format including . mha . The MITK visualization tool kit supports a bunch of medical image formats both reading and writing from one to the others.

However, you can save to .mha format directly BUT you need to use C++ ITK toolkit not Matlab.

Good Luck

How can I convert .mha (Medical) images to.jpg.MIPAV does not support .mha.anyone help please

Could you please tell me how have you converted .mha to .jpg .Thank You. @Neha Baraiya

You just need to use the 'imwrite' function and specify the format to be .jpg.

Attention: this will be only for one slice if u want to save all the slices, u need to use loop to repeat the 'imwrite' function with different names (e.g slice number).

Example:

imwrite( vol (:,:,10),  'slice10.jpg' );

The above code will save the slice no. 10 from the volume 'vol' with name slice10 and .jpg format

Thank You. it has been saved but when i open it with imshow. it appears as blank image.

This is most likely happening if you did not normalize the grayscale values of the input image.

You have to normalize the grayscale values in the range [0 255] before saving the image.

Best of luck

Thank you.  i will try this

In fact, the problem is not the code. The slice you are trying to show / save is blank slice that has no information. This volume has about 176 slices in which some are blank without any information and such slices are not representing the brain and you should not consider these slices in your processing for optimiztion.

If you tried to show/save another slice e.g. 80, you find the difference.

Good Luck

You can also perform the normalization of the grayscales using my Matlab function in the attachment.

Good Luck

Thank You Ahmed

i want to know about different views also like axial, sagittal and coronal.how can we get these views?

The volume usually has 3 dimensions each represents one plane. By changing the index of the dimension variable, you will be able to show different planes.

The change in third dimension will show the axial plane, second dimension will show the coronal plan while the first one will show the sagittal plane.

This is one example applies for your case:

figure,imshow(squeeze(I(:,:,80))); title('Axial slice')

figure, imshow(squeeze(I(:,80,:))); title('Coronal slice')

figure,imshow(squeeze(I(80,:,:))); title('Sagittal slice')

Attention, you may need to use some functions to have real view of the images such as flipud, fliplr, rot90 ..........etc

Thank You Ahmed

how to write a 2D slice with .mha format

Saving 2D slice with mha format is somehow useless as you mha format is useful in case of 3D images. However, you still can do it by saving the image with .raw format (mhd) then use MITK to save to any other format such as .mha, nii, nifti, nrrd, ....etc

@Ahmed Elazab : How can I view the image of the entire brain from .mha slices?

I have downloaded the BRATS 2013 datasets. One .mha file contains so many slices. Which slice is to be used for tumor detection for the challenge? 

@Ahmed Elazab: I have downloaded BRATS 2013 dataset. There are multiple slices in one .mha file. Which slice is to be consider for segmentation?

you needed to consider all individual slices and work separately on each of them. Then you can combine them using slider in gui

@Neha Baraiya: Thanks Neha. Please suggest the gui by which I can do this.

Hi .can someone send me database for MRI brain images with tumor to [email protected]?

Dear Ahmed Elazab 

I used visualization-MITK workbench2016.11.0 software, but it has not an option to convert from .mha to .raw. 

Can you provide me the Brain MR images database.My email id is [email protected]

You can check the previous answers. You will find what you are looking for in the previous comments.

The mitk software doesn't provide the option to convert it into .raw format are there any alternatives to do this? Please provide the link

You can save it as .mhd , this option produces 2 files, one of them the .raw format you want.

Good Luck

I have BRATS database and MITK software can you help me how to convert from .mha into .raw format using MITK software

Dear all,

It seems many guys are confused although it is extremely easy. There is no .raw format when u try to save the file but choosing to save it as .mhd will produces 2 files, one of them the .raw format you want. The other is .mhd which represents information about the image such as dimensions, types, spacing ...etc, this is simple text file u can open with Notepad.

Good Luck

Is the second file .zraw format is the same you are talking about .raw format and when reading the file it's showing the error as "RescaleSlope not available, assuming 1

RescaleIntercept not available, assuming 0".Help me to recover from this problem

When you choose to save " MetaImage(*.mhd) ", the output will not be .zraw which is compressed raw file produced by some other tools such 3D Slicer. The output in the case of MITK will be .mhd and .raw which is just the raw image file without any compression.

I got 2D slices from 3D image. I got struck on which slice I have to perform segmentation and feature extraction

I am also facing same promblem i.e reading of mha format image in to matlab. please, Can any one help me in this regard? thank you.

@Srinivas B.

Please refer to the previous answers. You will find the solution of how to read mha format.

Good Luck

Srinivas B.

You can use following lines of code to access mha files in MATLAB using the function attached. :

info1=mha_read_header('path of any modality');

v1=mha_read_volume(info1);

I1=mat2gray(v1(:,:,slice_number));

imshow(I1)

During execution this code I'm facing this error please check this:

Invalid field name: 'dim[0]'.

Error in mha_read_header (line 78)

info.(type)=data;

@ Shiv Naresh Shivhare

Dear Javaid ,

The code shared above is correct. You may have entered the incorrect file path. Please check the full path of mha file with proper extension to pass inside the mha_read_header.

In addition you can directly run the function "viewer3d" on the Command Window and select the file path in order to visualize any specific MRI modality.

I hope it will help.

my dicom file is getting saved as .mhd and .zraw files but not .mhd and .raw. how to convert .zraw to .raw?

@Neha Baraiya

First you can add these functions into matlab directory.

Then you can use thwe following code in matlab.

clc;

clear;

close all;

info = mha_read_header('VSD.Brain_3more.XX.O.OT.54517.mha');

data = mha_read_volume(info);

for i=1:155

imshow(data(:,:,i),[]);pause(0.01);

end

Anita Khanna

Check my previous answers and follow the steps therein.

Good Luck

I am impressed that people are discussing BRATS related things also here. I would like to add that if you are a Python user I tested the data with MedPy and I advice this library

Alessandro Crimi hi can you share the code

with me

Try this

https://www.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3d

You can use the function "ReadData3D", it supports the following formats :

Dicom Files ( .dcm , .dicom ) V3D Philips Scanner ( .v3d ) GIPL Guys Image Processing Lab ( .gipl ) HDR/IMG Analyze ( .hdr ) ISI Files ( .isi ) NifTi ( .nii ) RAW files ( .raw , .* ) VMP BrainVoyager ( .vmp ) XIF HDllab/ATL ultrasound ( .xif ) VTK Visualization Toolkit ( .vtk ) Insight Meta-Image ( .mha, .mhd ) Micro CT ( .vff ) PAR/REC Philips ( .par, .rec)

You can read .mha (Medical) images in MATLAB by:

function data = mhd_read_image(filename)

info = mha_read_header(filename);

data = mha_read_volume(info);

Or you can use the function "ReadData3D", it supports the format .mha

Code matlab in this link:

https://www.mathworks.com/matlabcentral/answers/87755-how-to-read-display-and-process-mha-files-in-matlab

data = mha_read_header(image_folder_name);

V = mha_read_volume(data);

imshow(squeeze(V(:,:,round(end/2))),[]);

image_folder_name is the image folder. it should be in your working directory.