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.

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 
                      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 Red Hat 9 and Mac OS X can be downloaded here: CTN-Mini.tar.gz.

The necessary NIfTI header files and precompiled library files for Red Hat 9 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