NYU CBI DICOM to NIfTI Converter

The dinifti program converts MRI images stored in DICOM format to NIfTI format.

License

dinifti is licensed under the standard BSD license.

Current version:

2.32.1, released October 21, 2013.

Download

Mailing List

A dinifti mailing list is hosted by the center. The list is for announcements, features requests and to indicate bugs. To subscribe to the list, please visit the page http://cbi.nyu.edu/mailman/listinfo/dinifti.

Usage

The program can convert single files, a list of files or a whole directory. If any of the input files are not in DICOM format, an error message will be printed, but the program will continue.

Usage: dinifti [OPTION] <DICOM input> <NIfTI output>

Options:
 -g                   compressed output
 -f <output format>   'a2' - ANALYZE 7.5 Dual file
                      'n2' - NIfTI-2 Dual file
                      'n1' - NIfTI-1 Single file  **Default**
 -d                   append series description to output file name(s)
 --name="<format>"  format output file name(s) according to <format>
                      where <format> : 
                                       %I = subject ID
                                       %N = subject name
                                       %S = series number
                                       %D = series description
                                       %Y = series date
                                       %T = series time
                                       %A = accession number
                                       %C = image comments
                                       %% = percentage sign
                      Example: 
                               --name="%Y:%T - %A - %I - %D(%S)"
                      will result in name(s) formed like
                               date:time - accession - ID - description(number)
                      N.B.: format string must be enclosed in quotes
                            if format is specified, -d flag is ignored
                            the reserved character "/" will be rendered as "~"
 -s #                 number of slices per volume
 -v --verbose    enable verbose status output
 -n --noact      do all processing, but do not write files

 -h --help       print this help and exit
 -V --version    print version number and exit

I/O Options
 <DICOM input> can be single file, list of files or directory
 <NIfTI output> can be single file or directory

Dependencies

DICOM: the CTN library developed by the Mallinckrodt Institue of Radiology, Washington University in St. Louis MO, http://erl.wustl.edu/.

NIfTI: the C reference implementation nifticlib developed by the NIfTI project, http://nifti.nimh.nih.gov/.

Build Instructions

A subset of the CTN header files and libraries is needed in order to compile dinifti.
The header files and precompiled library for Fedora 14 32-bit, CentOS 5.6 64-bit and Mac OS X can be downloaded here: CTN-Mini.tar.gz.

The necessary NIfTI header files and precompiled library files for Fedora 14 32-bit, CentOS 5.6 64-bit and Mac OS X can be downloaded here: NIfTI-Mini.tar.gz.

dinifti is build using cmake (comes with many OS distributions, or can be downloaded from http://cmake.org.

If all of the include files and libraries where unpacked under a common root (e.g., includes in /usr/local/include and libraries in /usr/local/lib):

$ cd DICOMNIfTI/build
$ cmake -D PREFIX:PATH=/usr/local ..
$ make
If the include file and libraries where unpacked under different directory roots (e.g., includes in /developer/include and libraries in /shared/lib):
$ cd DICOMNIfTI/build
$ cmake -D INCLUDEDIR:PATH=/developer/include -D LIBDIR:PATH=/shared/lib ..
$ make