have a file with .nii extension. I don't know how to convert a .nii file into 2D format.My question is while converting .nii file into 2D, am I losing some information about the file.Which format is good? dicom or png or bmp.
nii = load_nii('im.nii');
size(nii.img);
returns
ans =
39 305 305
and it is in uint8 format
May I use squeeze or resize?How to apply resize to this image;whether it lose information?
Here you go my friend, enjoy.
https://github.com/alexlaurence/NIfTI-Image-Converter/
I recomend you, download ITK-SNAP (http://www.itksnap.org/pmwiki/pmwiki.php) for open the nifti (.nii) image.
The next step, is save in a document the relevant information of the image that you can found in "tools/ image information" in ITKSnap, (Voxel spacing, Dimensions, Origing and orientation).
Finally you need save the image (File/Save Image/Main Image) with the format "MetaImage" that is the .raw format, and then you can read this file without problem in matlab, with the next code.
file_name = 'image.raw'
Information = fopen(file_name,'r')
IM = fread(Information,'int16')
IM = reshape(IM,[Dimensions]); % You can extract the dimension values from ITKSnap
Then if you want you can save the information in the format that you need.
IM = reshape(IM,[39,305]);
Error using reshape
To RESHAPE the number of elements must not change.
Also how to display the same image?
You can send me the image file to see what happen with the dimensions.
Regards
I have a NIfTI to DICOM converter that might or might not help you. With Google, I found a "Nifti toolbox for MATLAB" that also might be of use (I haven't tried it). See the links below.
http://www.dclunie.com/pixelmed/software/javadoc/com/pixelmed/convert/NIfTI1ToDicom.html
http://www.dclunie.com/pixelmed/software/
https://www.sites.google.com/site/kittipat/mvpa-for-brain-fmri/convert_matlab_nifti
With the conversion from nii to .IMG; it doesn't combine different images such that they are 2 or 3D
I wrote a tool to help you. It takes a .nii file (3D or 4D), and flattens it to a png file for every single slice (in all volumes for 4D data), renames all the png files for you so that you keep slice and vol info in these images. Enjoy!
https://github.com/alexlaurence/NIfTI-Image-Converter
Hi there,
Thank you so much. This converter is not for MatLab..is for Python..
I would need that program! Any possibility that it can be a MatLab code.
Kind Regards,
Gurjit
I'm a bit rusty on Matlab since graduating, I could port it for Matlab. But out of curiosity, why do you need it for Matlab in particular? Can't you just run my script and get your images?
Here you go my friend, enjoy.
https://github.com/alexlaurence/NIfTI-Image-Converter/
Thank you so much Alexander. I will check this out. I really appreciate your time.
Kind Regards,
Gurjit
Alexander Adam Laurence Can you kindly add the code for for 2D images too.
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