Opening .nii files with MATLAB (or, converting .nii to .hdr + .img files)

[Guy]

I need my images loaded into MATLAB for analysis. My programmer is
having trouble loading the .nii segmentation file and has asked me to
save my files as .hdr and .img, which he says MATLAB can read

My questions are:

1. Is there an easy way to convert a file saved as .nii to .hdr
and .img files?

or

2. Is there a way for MATLAB to read the .nii files?

Thanks,
Guy

[Mark Pearson]

Guy wrote:
> I need my images loaded into MATLAB for analysis. My programmer is
> having trouble loading the .nii segmentation file and has asked me to
> save my files as .hdr and .img, which he says MATLAB can read
>
> My questions are:
>
> 1. Is there an easy way to convert a file saved as .nii to .hdr
> and .img files?
>

You could try using medcon http://xmedcon.sourceforge.net/ which
supports conversion between many formats including nifti and analyze.

--
Mark Pearson BSc (Computing)
Technical Support, Dept Nuclear Medicine
Concord Hospital, Hospital Road, Concord, NSW 2139, Australia
Phone:+61-2-97676339 or +61-297677450; FAX:+61-2-97677451

[Vince Hradil]

http://www.mathworks.com/matlabcentral/fileexchange/8797

[Tom Schoenemann]

Even easier:

1) Open the file in ITKSNAP: File>open>greyscale

2) Save the file in Analyze format (paired .hdr and .img files).  File>save>greyscale; in the dialog window that opens, enter the name you want to save the file as in the Filename box, but instead of using .nii at the end use .hdr  (e.g., instead of image.nii, make it image.hdr).  This will automatically change the Image File Format to 'Analyze' (which is what you want).

One issue: it seems to reorient the file (at least it did with me).  I think this is because Analyze doesn't deal with orientation in a consistent way (I've even had the same file open left-right reversed on different computers, even though they were both running the same image processing program!).

-Tom

_________________________________________________

P. Thomas Schoenemann

Assistant Professor of Anthropology

Department of Sociology & Anthropology

MSC 7501

James Madison University

Harrisonburg, VA  22807

Phone: (540) 568-6243

E-mail: scho...@jmu.edu

Open Research Scan Archive at Penn Co-Director

Consulting Curator and Research Associate

Museum of Archaeology and Anthropology

University of Pennsylvania

Philadelphia, PA 19104-6398

Phone: (215) 573-7671

E-mail: ptsc...@sas.upenn.edu

Homepage: http://www.sas.upenn.edu/~ptschoen/

[Guy]

Thanks to for all replies.

Guy

> E-mail: schoe...@jmu.edu

>
> Open Research Scan Archive at Penn Co-Director
> Consulting Curator and Research Associate
> Museum of Archaeology and Anthropology
> University of Pennsylvania
> Philadelphia, PA 19104-6398
> Phone: (215) 573-7671

> E-mail: ptsch...@sas.upenn.edu
>
> Homepage:http://www.sas.upenn.edu/~ptschoen/