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Siemens DICOM sort and convert to NIfTI

version 1.8 (166 KB) by

Converts Siemens MRI DICOM data into NIfTI format, and/or anonymises and sorts into scan directories



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The program offers GUI (dicom_sort_convert_main.m) and .m (example_dscm_call.m) input to select input and output directories and determine options. The main functions are

i) sorting of Siemens MR scanner (IMA) data into directories, removal of patient name from file, and lightly anonymisaton (only PatientName fields but not DOB, gender, PatientID, etc)
ii) Conversion to one-file (.nii) or two-file (.img, .hdr) NIfTI format (one per scan), reformatting more complex scans to use up to six dimensions of the NIfTI structure (time-points, echo, RF channel, phase/magnitude, diffusion gradient, etc). Also writes both DICOM header info and the text section of Siemens header info to a text_header.txt file for each scan.
iii) Generation of a list of all scans performed (scan_list.txt) including most relevant parameters (can easily be customised), making it easy to generate a summary sheet for each subject scanned.

The programs are dependent on file nomenclature which contains the scan number and other required parameters separated by a number of full stops. I’m not sure if it’s feasible to get this to work for MR data from other manufacturer’s. If it doesn’t work for your scanner feel free to get in touch (before leaving feedback would be nice) and I could have a look if it makes sense to try to make it more flexible.

Thanks to Jimmy Shen for sharing, developing and supporting his excellent NIfTI toolbox.

Comments and Ratings (3)

Cath H

Cath H (view profile)

Thanks for sharing this - my previous converter was having some serious issues with some exported files, but this handled them with ease!



Elmar (view profile)

thanks for sharing simon, this really helped!



Please see version changes via 'help dicom_sort_convert_main.m'.


please see help


Summary field too short to be useful. Use >> help dicom_sort_convert_main


The 250 character limit for summaries is too short.
download and type >> help dicom_sort_convert_main to see changes in v1.17


There were a couple of trivial bugs in v1.15 which rendered it a defunct version. I have corrected these. Apologies


Splash image (required) was missing from archive


v1.14 1) reformats DTI data, 4th dim is grad
v1.15 1) Suggests alternative directory names if illegal
2) Improved reformatting to [x][y][z][time][echos][channels][phase/mag] for 8, 24 and 32-element coils


v1.14 1) reformats DTI data (4th Dim is grad)
v1.15 1) Suggests alternative directory name if illegal chars
2) Improved reformatting into [x][y][z][time][echos][channels][phase/mag] for 8, 24 and 32-element coils

MATLAB Release
MATLAB 8.1 (R2013a)

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