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DICOM to NIfTI converter

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DICOM to NIfTI converter

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09 Aug 2013 (Updated )

dicm2nii.m converts dicom files into nifti files.

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Description

dicm2nii.m converts dicom files in a zip file or in a folder (including sub-folders) into nifti files. It can also convert Philips PAR/REC files and AFNI HEAD/BRIK files into nifti files.
Features:
1. Support nii(.gz) and hdr/img(.gz) output.
2. Create bval and bvec files if there is DTI series.
3. Store B0 unwarping parameters in nifti header, such as delta TE for fieldmap, and effective echo spacing, TE and phase encoding direction for EPI data.
4. Store slice timing related information in nifti header (except for Philips).
5. Unique and descriptive result file names.
6. Several useful dicom functions, like reading header or image, sorting dicom files, renaming dicom files, are included.
'doc dicm2nii' or 'help dicm2nii' for details and usage.
Run dicm2nii without argument will evoke graphic user interface.
Bug reports, comments and suggestions are welcomed.

MATLAB release MATLAB 8.1 (R2013a)
MATLAB Search Path
/
Other requirements dicm2nii.m requires NIfTI toolbox. For easy distribution, the required NIfTI code is included. Thanks Jimmy Shen for the excellent toolbox.
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Comments and Ratings (13)
24 Sep 2014 Xiangrui Li

Dear Macro,
Thank you for the error report, and for sending me the file for diagnose.

The problem is caused by some 3rd party dicom converter, which loses the VR info for vendor-specific tags (private tags) during the conversion. Without correct VR, these tags are not correctly interpreted by dicm2nii.

I guess the problem reported by JuanesA89 is likely the same cause.

We now know that GDCM and DicomVCL.com converters, at least some versions of these converters, may cause this problem.

So the suggested solution is to use original dicom data from scanner without other conversion.

-Xiangrui

23 Sep 2014 Marco Rotonda

Hi Xiangrui,
I'm trying to load some dicom files with dicm2nii.
With general gui I have this error (I'm copying all the command window):

dicm2nii
Xiangrui Li's dicm2nii (feedback to xiangrui.li@gmail.com)
Validating 20 files (GE) ...
Converting 1 series into .nii.gz: subject R A
Cor_T2_FRFSE 20

In an assignment A(I) = B, the number of elements in B and I must be the same.

Error in dicm2nii (line 625)
for j = 1:dim(3), t(j) = tryGetField(h{i}{j}, flds{ind}, nan); end

Error in dicm2nii>dicm2nii_gui (line 1688)
dicm2nii(src, dst, rstFmt, mocoOpt, subjName);

Error in dicm2nii (line 224)
dicm2nii_gui(dataFolder); % mis-use first two input for GUI


Error while evaluating uicontrol Callback

This is what I have if I give a more specific instruction:
dicm2nii('/Users/blond/Documents/NIC/AR/SER006', '/Users/blond/Documents/NIC/AR/SER006/corrected',1,1);
Xiangrui Li's dicm2nii (feedback to xiangrui.li@gmail.com)
Validating 24 files (GE) ...
Converting 1 series into .nii.gz: subject R A
Cor_T2_FRFSE 20
625 for j = 1:dim(3), t(j) = tryGetField(h{i}{j}, flds{ind}, nan); end

In an assignment A(I) = B, the number of elements in B and I must be the same.

Error in dicm2nii (line 625)
for j = 1:dim(3), t(j) = tryGetField(h{i}{j}, flds{ind}, nan); end

Any idea?

Thanks in advance.

Marco

31 May 2014 peter888

the dicm2nii tool is very useful...
thanks Dr Xiangrui Li.

27 Jan 2014 Xiangrui Li

Hi Paul,
Thank you for the comments and suggestions.

Now the missing file check is not as strict as before. For Philips data, this check is skipped due to the possible sparse instance numbering. For other vendors, missing files at beginning is allowed now.

The bug in save_dti_para is fixed.

The converter can deal with dicom files without meta info now.

Cheers.

-Xiangrui

19 Jan 2014 Paul Groot

Hi Xiangrui,

Nice work! I just converted a bunch of PAR/RECs and a single DICOM series containing Philips DTI data. All PAR/RECs seem to be OK, so that's really nice. However, I had to change a few lines to get it working for the DICOM files.

One issue has to do with the instance numbering of the DICOMs. Our DTI series have sparse instance numbering. So, instead of skipping the series at the line where it prints a line about a missing instance file, I inserted the following:

H = h{i}; % cell array containing empty elements
h{i} = H(~ind); % only keep the non-empty ones

The second thing I had to modify, was the Manufacturer test in function save_dti_para. It seems that structure s initially contains a rather complete DICOM header, but when the for-loops continues, the structure is replaced by a reduced DICOM header that doesn't contain the Manufacturer string anymore. The solution is to store the manufacturer string in a separate variable, or to keep a separate copy of the initial structure s.

I also noticed that the DICOM reading part is very strict when it comes to PART10 compatibility. If the meta header is missing, it will report an unsupported file format. Strictly speaking, this is true, but a lot of (older) applications don't store the meta header at all.

Thanks for making these scripts available.
Paul

21 Nov 2013 Xiangrui Li

Hi JuanesA89,
The error means number of slices extracted by the code is not a single number, which is odd. If you don't mind, you can send me one of your dicom files, or dicom header of a file returned by hdr = dicm_hdr(dicmFileName).

-Xiangrui

21 Nov 2013 JuanesA89

Hi Xiangrui,
I used your code for converting a dicom file to a nii. And I get this error:

"Operands to the || and && operators
must be convertible to logical
scalar values.

Error in dicm2nii (line 493)
if ~isempty(nSL) && nSL>1

Error in dicm2nii>dicm2nii_gui
(line 1469)
dicm2nii(src, dst,
rstFmt, mocoOpt,
subjName);

Error in dicm2nii (line 168)
dicm2nii_gui(dataFolder); %
mis-use first two input for GUI

Error while evaluating uicontrol Callback"

Can you help me? Thanks

15 Nov 2013 Xiangrui Li

Hi Qingyan,
I just did an update last night, and it may be available sometime today. I believe it should get bval/bvec from your PAR file. If no, please let me know.
-Xiangrui

15 Nov 2013 Qingyan

Hi,
I used your code to convert a DTI par file. I don't have any error, but it didn't give me the bval/bvec file either.
I have par v4.2 file.
Any suggestion?

03 Oct 2013 alexandre obert

Hi,

I think it's a v4.2 Par file.

Thx

02 Oct 2013 Xiangrui Li

Hi O.A,
Thank you for the feedback. I realize it is because fullfile in older Matlab doesn't support cellstr input. Now I use strcat to fix the issue. Please wait for the next update to be available.

Also I tested only V4 of PAR file. In case of PAR file parsing problem, please send me a PAR file if yours is not V4.

-Xiangrui

02 Oct 2013 alexandre obert

Hi,

I would like to use your converter to convert rec/par files to nifti but when I use dicm2nii GUI, it says this :

Undefined function 'eq' for input arguments of type 'cell'.

Error in fullfile (line 37)
if (f(end)==fs) && (part(1)==fs),

Error in dicm2nii>dicm2nii_gui (line 1311)
src = fullfile(folder, src);

Error in dicm2nii (line 146)
dicm2nii_gui(dataFolder); % mis-use first two input for GUI

Error while evaluating uicontrol Callback

Any advice ?

Regards,

O.A.

27 Sep 2013 Xiangrui Li

The test on GE/Philips data was based limited dataset. Please report problem to author if there is any problem.

Updates
09 Aug 2013

Some minor improvement for the code. Add a line for usage.

19 Aug 2013

1. Allow to specify a subjectID for nii;
2. Accept more input source options, like 1 or more dicom files, or wildcard like run1*.dcm;
3. Include related NIfTI toolbox code in the m file for easy distribution.

21 Aug 2013

1. File name is changed from dcm2nii.m to dicm2nii.m. This will avoid confusion with MRICron's dcm2nii converter.
2. GUI is implemented.
3. Bug fix for cellstr input for multiple files.

26 Aug 2013

Some SPM users may not have Imaging Processing Toolbox. This update removed this dependency. This also speeds up the dicom header parsing.

27 Aug 2013

A bug fix for '*' input, and some minor improvement for dicom header reading

06 Sep 2013

1. Try and suggest to use pigz for gz compression
2. Fix the missing-field error for DTI data with more that one excitations.
3. Protect GUI from command line plotting.

09 Sep 2013

Bug fix for DTI bval/bvec files introduced in last update

25 Sep 2013

Major: first implementation for conversion of GE and Philips data.
Minor: remove dependency on normc, etc.

02 Oct 2013

1. Works for Siemens non-mosaic DTI data too.
2. Make xform matrix robust, aiming to work for Philips single dicom file (no data for test though).
3. dicm_hdr can decode SQ now.
4. Avoid fullfile, since it doesn't accept cellstr in older Matlab.

07 Oct 2013

1. First working version for Philips multiframe dicom
2. Some tweaks to dicm_hdr
3. Minor bug fixes

17 Oct 2013

1. Support implicit VR dicom;
2. Make dicm_hdr, dicm_img and dicm_dict available to users by extracting them from dicm2nii. Add rename_dicm.
3. Improve dicm_hdr

21 Oct 2013

1. Minor improvement for dicm_hdr: read V4.1 PAR file correctly;
2. Make some MRI parameter non-mandatory, so may work for other modality.

30 Oct 2013

1. Implement conversion for AFNI HEAD/BRIK files.
2. Bug fixes for dealing with current folder as src folder etc.

15 Nov 2013

1. Bug fix and improvement for DTI parameters.
2. Deal Philip multi-frame B0 map correctly.
3. Great speed improvement for multi-frame dicom.

21 Jan 2014

Majors:
1. skip missing file check;
2. Allow missing files at the beginning of a series.
Minors:
1. Bug fix for DTI parameter parsing;
2. Also save error info into a file;
3. Other minor improvements.

27 Jan 2014

1. Support dicom without meta info;
2. Bug fix for gzip.m detection;
3. Fix problem with ~ as home folder;
4. Improvement for error info file.

06 Feb 2014

1. bug fix for MoCo series detection;
2. bug fix in rename_dicm: missing Manufacturer

20 Mar 2014

1. Store FSL slice timing in dcmHeaders.mat;
2. Implement slice timing for multiband dicom;
3. Bug fix for slice order for some GE data;
4. Other minor improvements;

25 Mar 2014

Not set cal_min and cal_max anymore, so avoid display range problem.

07 May 2014

1. Fix to work for new GE data, including DTI;
2. Improved multi-subject data conversion;
3. Better file name for GE/Philips data;
4. Many minor fix and improvement.

21 May 2014

1. Image storage change to make DTI data work for FSL 5.05 and later
2. Change phase direction in image space for FSL
3. Use ProtocolName for Siemens data
4. GE data: can get phase direction for later version; take care of interleaved numbering

11 Jun 2014

1. Take care of non-unique ixyz;
2. Bug fix for slice_code for interleaved descending;
3. Bug fix for GE interleaved file order;
4. Store readout for DTI.

18 Jul 2014

1. can deal with compressed tgz, tar file
2. some minor fixes

25 Jul 2014

1. Fix the problem caused by PAR 4.2 keyword case change;
2. Ignore PAR file extension case.

24 Sep 2014

1. Take care of missing VR by some 3rd party dicom converter;
2. some minor improvements.

09 Oct 2014

Take care of different carriage return issue in Philips PAR file

16 Oct 2014

1. Include new file sort_dicm, which sorts files for different subjects into sub-folders;
2. Remember the GUI setting from last conversion;
3. Other minor improvements.

16 Oct 2014

Optional output argument for sort_dicm

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