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Paul Groot

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Academic Medical Center Amsterdam

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29 Jan 2014 Screenshot Anonymize Siemens rda-files Remove or modify metadata from native Siemens MRS files Author: Paul Groot mri, deidentification, pseudonimization, anonimization, siemens, mrs 10 0
  • 5.0
5.0 | 1 rating
05 Jun 2013 Screenshot Reading Philips MR Physiolgy logfiles ReadPhilipsScanPhysLog.m reads Philips scanphyslog files, which are created by Philips MRI scanners. Author: Paul Groot mri, philips, physiological, data import, biotech, image processing 15 0
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03 Jun 2014 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen

Hi Sangeetha,

About the LAPACK loading error: (dlopen: cannot load any more object with static TLS)

This is a known issue on linux systems with matlab versions R2012b and higher, and is not related specifically to this toolbox:

http://www.mathworks.de/support/bugreports/961964

It seems there is a new workaround, but a previous suggestion was to add the following line to startup.m:

ones(10)*rand(10);

This makes sure that the relevant libraries are loaded at startup, which did the trick on our systems.

Paul

19 Jan 2014 DICOM to NIfTI converter dicm2nii.m converts dicom files into nifti files. Author: Xiangrui Li

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

20 Jun 2012 Read Medical Data 3D GUI to open most Medical file-formats: Dicom, V3D, ISI, NifTI, Analyze and other formats Author: Dirk-Jan Kroon

atie,

First make sure to add the PAR/REC scripts to your path:

addpath('...\ReadData3D\par');

(or copy them to your current script folder)

Then just read the data in two stages:

info=par_read_header('filename.PAR')
data=par_read_volume(info);

The info struct is a collection of all the information in the PAR file. That's it!

11 Sep 2009 freehanddraw Draw smooth lines freehand on images or plots; return the handle and xy data of the line object. Author: Brett Shoelson

Very nice work!
Noticed a small issue, which may only occur in recent (R2009a) releases: The DoubleBuffer property seems not always present in the oldvals structure at line 82. This could be solved by moving it to a separate line:

if isfield(oldvals, 'DoubleBuffer')
set(gcf,'doublebuffer',oldvals.DoubleBuffer);
end

28 Aug 2009 settings Interact with Windows registry from MATLAB. Author: Mihai Moldovan

Nice function! I think there is a minor issue with the double backslash escaping. You can get rid of all the double backslashes by changing the fprintf-line from:
fprintf(fid,t)
to
fprintf(fid,'%s\n',t);

Comments and Ratings on Paul's Files
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19 Jun 2014 Anonymize Siemens rda-files Remove or modify metadata from native Siemens MRS files Author: Paul Groot kyathanahally, Pruthviraj

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