Hello!

I am reading a nifti file obtained using dcm2niix from a set of 3DT1 images from a GE scanner.
Dcm2niix doesn't seems to produce any error nor warning (even in verbose mode).
However, the image seems stretched in the z-direction, which is also the slice direction (i.e. the 3DT1 was acquired in axial mode).

Note that opening the exact same nifti file with another viewer such as FSLEyes goes perfectly fine... by clicking "Info" I get the same slice number (about 300) and dim3 size (0.5mm) than using MRIcron.

Tested with MRIcron, latest version on MacOS and Linux (Ubuntu). Conversion done on Ubuntu with latest version of dcm2niix.

Please find a screenshot attached to this message.

Best

Antonin Rovai

Sounds like a variation of issue 386 https://github.com/rordenlab/dcm2niix/issues/386, e.g. GE's interpolation of 3D datasets. Note that both MRIcron and FSLeyes use dcm2niix to convert DICOM images, so this reflects which version of dcm2niix you are using. The latest developmental release (and upcoming stable release) should fix this. You can always put the developmental release of dcm2niix in your MRIcron Resources folder to use it instead of the version that ships with your software.

If this does not resolve your issue,  please post an issue on Github.

For future acquisitions, I strongly encourage disabling the interpolation on the console. Interpolation requires more disk space and will disrupt some post processing (mrdegibbs).

Hello,

I used the same version of dcm2niix for both images because I directly opened the nifti in FSLEyes and MRIcron. Dcm2niix was used before that, in command line mode, not using any GUI.

At any rate:
- I'll wait for the next release
- I'll disable interpolation on the console

Thanks
Antonin

Oh, sounds like it is just an anisotropic image. Did you try going to MRIcron's Help/Preferences window and choosing "Reorient images when loading" and reloading the image? You may also want to try MRIcroGL which is able to leverage modern hardware.