questions > RE: Issue converting dicom to nifti for diffusion GE data
Jul 24, 2024  11:07 PM | Chris Rorden
RE: Issue converting dicom to nifti for diffusion GE data

Amy


 


Thanks for the sample dataset. The problem is described here


  https://github.com/rordenlab/dcm2niix/is...


This problem is now fixed in the development branch - and will be included in the next major release. In the mean time, you can compile your own copy of the development branch. As a bonus, if you build with the USE_OPENJPEG option it will convert your rare DICOM compression transfer syntax. So the steps would be:


git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
cd dcm2niix
mkdir build && cd build
cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
make
cd bin
./dcm2niix /path/to/dicoms


This was a very unusual sequence, with a lot of derived images and RGB colored screenshots. Since the software version was stripped from the DICOMs, you will need to  manually insert the slice timing fields into your EPI data. You may want to check the provenance of these images to see why the public software version tag was removed from your data - that is helpful for audits and to control variability. Beyond these points, the images themselves look terrific - the GE Premier's name is truth in advertising.

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TitleAuthorDate
Amy Jolly Jul 19, 2024
RE: Issue converting dicom to nifti for diffusion GE data
Chris Rorden Jul 24, 2024
Amy Jolly Jul 26, 2024
Chris Rorden Jul 26, 2024
Amy Jolly Jul 24, 2024
Chris Rorden Jul 19, 2024
Amy Jolly Jul 24, 2024