Nifti file orientation stitching

[Nidia Heredia]

I'm new to Itk-snap and have some previous experince with 3d slicer and DICOM files. I was told to use itk snap and nifti files for to save time.  I am trying to upload my nifti files to begin analysis. However my files for brain MRI are divided into axial, coronal, and sagittal. I tried just open the entire folder for the singular individual, but it made me choose from one of the orientations. Can anyone point me to some resources that will help me go in the right direction so I can properly view the MRI scans

[Jilei Hao]

Hi,

Can you share a screenshot or a screen recording for us to understand your issue better? Also the version of ITKSNAP and your operating system.

Thanks,

Jilei

[Nidia Heredia]

Hi, 

So, I realized that I was looking at a set of scout images instead of the actual images I'm collecting data on. However, I hit another wall.

 I had forgotten that we had taken two sets of images of our brains to stitch together post scan.We had originally stitched these together as dicoms to get the full brain. When I upload the stitched dicom file to Itk-snap however the quality is terrible and I get a warning message about possible loss of precision. Is it possible to stitch my  nifti files through itk snap at all?

<-warning message<-nifti quality

Best,

Nidia

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[Jilei Hao]

Hi Nidia,

Thanks for the screenshots!

About the warning: it only means the combined file stores its intensities as 64-bit ("double") numbers. The version of ITK-SNAP you're using keeps those values exactly, so nothing is lost, and the warning isn't what makes the image look bad. The message is out of date, and we'll fix it.

To work out the quality problem, could you tell us a bit more about how you combined the two DICOM series?

• What software or steps did you use?
• Do the two sets of images overlap?
• Which version of ITK-SNAP are you using (Help → About)?

If you can share the combined DICOM, or the two original series, we can also take a look directly.

On stitching the NIfTI files: ITK-SNAP itself doesn't have a stitching tool, but it comes with a command-line tool, Convert3D, that can do it. Once we know a bit more about your images, we can send you step-by-step instructions.

Best,

Jilei