Brain Image File Conversion/Import Tips for MATLAB
Moo K. Chung mkchung@wisc.edu
Department of Biostatistics and Medical Informatics
Waisman Laboratory for Brain Imaging and Behavior
University of Wisconsin-Madison
Analyze file format
December 5, 2007
Please
d/l and install
It is
the simplest way to view medical images one slice at a time.
Get image dimension from MRICRO and run the following code
fid=fopen('F213-18-07.img');
for i=1:711
[a,count]=fread(fid,512*512,'int8');
if i==427
b=a;
end;
end;
b=reshape(b,512,512);
imagesc(b)
It
will load the 427th image slice into MATLAB.
Now compare the loaded image with MRIcro display.
AFNI file format
December 5, 2007
Converting
MINC to BRIK
/apps/linux/afni/3dMINCtoAFNI
This is the part of AFNI package
3. Converting BRIK to MINC
/apps/linux/afni/3dAFNItoMINC
This is the part of AFNI package
4. Loading BRIK into MATLAB
This is based on the AFNI MATLAB package written by Ziad Saad of
NIH.
BrikName='jacob2';
Opt.Format = 'matrix';
[err, image, Info, ErrMessage] = BrikLoad (BrikName, Opt);
%
image = 181 x 217 x 181
NIFTI file format
October 6, 2014
To read and write NIFTI file formats in
MATLAB, you need to download the following package.
To read a NIFTI file with file name sample.nii, run
nii =
load_nii('sample.nii)
Image is stored in nii.img. Image dimension can be obtained by
running
size(nii.img)
Saving volume image into NIFTI file is a bit
complicated. Header information (image size,
number formats etc) should be manually entered. Alteratively,
you can copy and paste the header information from other NIFTI
file formats. If you want to save image variable vol to NIFTI
file name vol.nii, run
output=nii
output.img = vol
save_nii(output, 'vol.nii')