MRI Brain Segmentation

Neuroimaging Case Study for seminars and webinars.

Description

This case study shows how MATLAB can be used for a medical imaging problem. Given an MRI scan, first segment the brain mass from the rest of the head, then determine the brain volume. Also compare portions of gray and white matter present. This example was developed for seminars. It was also used for webinars for medical applications broadcast live on May 6, 2004.

This package includes some MATLAB code and an MRI scan series consisting of 60 DICOM images. Note that this code relies on MATLAB Central submissions from others. Detailed references to those sources are included.

Acknowledgements

The author wishes to acknowledge the following in the creation of this submission:
Sliceomatic, hline and vline, data_marker

• Required Products: Image Processing Toolbox
• MATLAB release: MATLAB 7 (R14)
• Other requirements: * Requires 2 other MATLAB Central submissions. * At least 512MB physical RAM is strongly recommended to run this example.

Other Files

analyze_series8.m,
isinteger.m,
limits.m,
move_vline.m,
movex_text.m,
ReadMe.txt,
Series 8/I0000417_anon.dcm,
Series 8/I0000418_anon.dcm,
Series 8/I0000419_anon.dcm,
Series 8/I0000420_anon.dcm,
Series 8/I0000421_anon.dcm,
Series 8/I0000422_anon.dcm,
Series 8/I0000423_anon.dcm,
Series 8/I0000424_anon.dcm,
Series 8/I0000425_anon.dcm,
Series 8/I0000426_anon.dcm,
Series 8/I0000427_anon.dcm,
Series 8/I0000428_anon.dcm,
Series 8/I0000429_anon.dcm,
Series 8/I0000430_anon.dcm,
Series 8/I0000431_anon.dcm,
Series 8/I0000432_anon.dcm,
Series 8/I0000433_anon.dcm,
Series 8/I0000434_anon.dcm,
Series 8/I0000435_anon.dcm,
Series 8/I0000436_anon.dcm,
Series 8/I0000437_anon.dcm,
Series 8/I0000438_anon.dcm,
Series 8/I0000439_anon.dcm,
Series 8/I0000440_anon.dcm,
Series 8/I0000441_anon.dcm,
Series 8/I0000442_anon.dcm,
Series 8/I0000443_anon.dcm,
Series 8/I0000444_anon.dcm,
Series 8/I0000445_anon.dcm,
Series 8/I0000446_anon.dcm,
Series 8/I0000447_anon.dcm,
Series 8/I0000448_anon.dcm,
Series 8/I0000449_anon.dcm,
Series 8/I0000450_anon.dcm,
Series 8/I0000451_anon.dcm,
Series 8/I0000452_anon.dcm,
Series 8/I0000453_anon.dcm,
Series 8/I0000454_anon.dcm,
Series 8/I0000455_anon.dcm,
Series 8/I0000456_anon.dcm,
Series 8/I0000457_anon.dcm,
Series 8/I0000458_anon.dcm,
Series 8/I0000459_anon.dcm,
Series 8/I0000460_anon.dcm,
Series 8/I0000461_anon.dcm,
Series 8/I0000462_anon.dcm,
Series 8/I0000463_anon.dcm,
Series 8/I0000464_anon.dcm,
Series 8/I0000465_anon.dcm,
Series 8/I0000466_anon.dcm,
Series 8/I0000467_anon.dcm,
Series 8/I0000468_anon.dcm,
Series 8/I0000469_anon.dcm,
Series 8/I0000470_anon.dcm,
Series 8/I0000471_anon.dcm,
Series 8/I0000472_anon.dcm,
Series 8/I0000473_anon.dcm,
Series 8/I0000474_anon.dcm,
Series 8/I0000475_anon.dcm,
Series 8/I0000476_anon.dcm,
StepThru.m,
thresh_tool.m,
update_SliceOMatic.m

[wenshu lee]

it can help the students interested in the image processing.

[roopa m]

 

[yd ccec]

good ,i like it

[zj zhao]

ww

[S.Ravikumar sampathkumar]

 

[ee fzaf]

 

[George Theofilogiannakos]

 

[bahare vafadar]

 

[hamid reza imani]

 

[PAN QF]

 

[Sanaz negahbani]

program with Matlab software for leaf classification & image segmentation
thanks alot

[Jiang Yun]

It's helpful for my study in medical imaging. I've not been kowning that MATLAB could also deal with the DICOM files.

[Mohammad Ahmad]

 

[Muhammad altaf]

help ful for the study of MRI
I am in search for xray enhancement

[aftab muhammad]

no

[Roman Rodionov]

Excellent presentation as an introductory talk for those who start MRI analysis with MATLAB.
Thank you very much!

[l smith]

very good!

[Joseph Paul]

 

[chethana s s]

matlab codeing on brain image segmentation

[Jau-Jie You]

Good tutorial.

[basil abu-hijleh]

Very good coding for matlap brain image processing

[Dheeraj Chahal]

Excellent code

[mitali lembhe]

 

[FABIAN FORERO]

me sirve para el trabajo de grado

[nandy kidd]

getting the following error in R2007

??? Output argument "hout" (and maybe others) not assigned during call to "C:\Program Files\MATLAB\R2007a\toolbox\images\imuitools\imtool.m (imtool)".

Error in ==> imtool at 155
  close_all = nargin == 2 && ischar(varargin{1}) && ischar(varargin{2}) && ...

Error in ==> imview at 18
hh = imtool(varargin{:});

Error in ==> analyze_series8 at 53
imview close all

[rohit garg]

i wanted a code for segmentation of brain tumor from 2D MRI images.

[sajal chirvi]

 

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[mahima bansal]

Make it more explanatory. so that it could be efficient for a beginner.

[Fazl-e- wahab]

 

[shokrollah derafsh]

 

[Nandan S]

 

[sheldon]

your work is good. it is helping me a lot. but i am facing a small problem if i give input(dcm files) of larger size like 138 kb other than that you used is 129 kb. please help me out with this. i am using matlab r2008a. i get the error;

voxel_size =

    0.9375 0.9375 6.0000

  Name Size Bytes Class Attributes

  D 256x256x12 1572864 uint16

??? Index exceeds matrix dimensions.

Error in ==> analyze_series8 at 43
im = squeeze(D(:,:,i));

after the dicom files stored are read.

[Preeti]

i am getting the error in imtool and not able to remove even downloading the patch as advised. please help.