Converting Your Siemens DICOM Images Into MINC Format

If you are on this webpage, you are most likely looking for help on how to convert your CD or DVD of DICOM images from the BIC's Siemens MR scanners into MINC format.

The program that does this is called dcm2mnc (DICOM to MINC) and it can be executed by typing in the following at the command line on any BIC computer:

dcm2mnc   [options]   <input_files directory>   <output_files directory>

Your disc should have 1 or more directories named with 8 digits; these contain your images. It is recommended that you copy the contents from the disc to a local directory and run the conversion program on that local directory. The CD will also likely have a dicomdir file in the root directory, which you can ignore.

If you have more than one directory of images and the directory names start with 070987 for example, you can copy the files like so:

cp  -R  /media/cdrom/070987*  /data/localdisk/.

After the files have been copied, check that the number of files match. For example:

ls  -A  /media/cdrom/0709873/  |wc -w

and compare the result with:

ls  -A  /data/localdisk/0709873/  |wc -w

The "wc -w" counts the number of files in the directory. Hopefully the numbers match, and you're ready to convert them with the following command:

dcm2mnc  /data/localdisk/0709873/*  /data/output_dir/

The resulting filenames are long and cryptic. Here's how to decode them:


A Few Points To Consider:

1- Make sure that your output directory is not a subdirectory of your source files. And ensure that your input directory only contains the DICOM files which you wish to convert.

2- It is possible that you may have too many files in one directory that will exceed the shell's memory allotment for command line arguments. For example if you have over 3000 individual DICOM files in one directory which you would like to convert, you may get an error message complaining that the "Arg list is too long."

If this happens you can try to run the command in a slightly different way. Try the following when logged into the BIC:

find <path_to_input_DICOMS> | xargs -i dcm2mnc \{\} <output_dir>

3- The conversion program will only be able to convert raw, unprocessed DICOM images. This includes 3D T1 weighted anatomicals, localizers, BOLD fMRI images, and diffusion weighted images. dcm2mnc will crash if you attempt to convert images other than the ones just mentioned.

If you run into any difficulties with the conversion, please let us know by e-mailing Mike at Mike's e-mail address or calling the MRI lab at tel. 514-398-8547.