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Siemens DICOM sort and convert to NIfTI

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Siemens DICOM sort and convert to NIfTI

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22 Dec 2008 (Updated )

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

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Description

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.

Acknowledgements

Tools For N If Ti And Analyze Image inspired this file.

Required Products MATLAB
MATLAB release MATLAB 8.1 (R2013a)
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Comments and Ratings (2)
11 Jun 2011 Roberta  
29 Jan 2009 Elmar

thanks for sharing simon, this really helped!

Updates
22 Jul 2009

    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

22 Jul 2009

  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

23 Jul 2009

Splash image (required) was missing from archive

03 Aug 2009

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

15 Jun 2010

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

16 Jun 2010

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

18 Apr 2011

please see help

29 Jan 2014

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

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