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Re: [Seg3D] NIfTI handling

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  • From: Jason Wiemers <>
  • To:
  • Subject: Re: [Seg3D] NIfTI handling
  • Date: Tue, 5 Jan 2016 22:50:46 -0600

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On Jan 5, 2016, at 10:46 PM, Ayla Khan <> wrote:

Hi Kabi,

Seg3D uses ITK's image reader to read NIfTI files, and also uses the same LPS (Left, Posterior, Superior) 3D basis. STL files are exported with the triangle surface oriented using this basis as well. I'm not familiar with FSLView, however I can add NIfTI to the set of file formats that we export through ITK in the next release.


On Dec 30, 2015, at 3:25 PM, Kabilar Gunalan wrote:

Hi Seg3D2 developers,

I am trying to use Seg3D2 to edit volumes that outline a given structure in a MRI and have found this tool to be extremely powerful and easy to use.  However, I need this data saved as a NIfTI file format (*.nii.gz).  I have tried to import the volumes as a NIfTI file format, edit them, and then export them as a NRRD file (*.nrrd).  I then use 3DSlicer to convert them to the NIfTI file format.

When viewed in 3DSlicer the NRRD file is oriented correctly and when viewing the NIfTI file (exported from 3DSlicer) in Seg3D2 it is oriented correctly.  However, when viewed with FSLView this NIfTI file is oriented incorrectly (possibly a x- and y-flip).  I have also found there to be flipping issues with Seg3D2 when exporting meshes (created from an isosurface of a volume imported as a NIfTI file) as a STL file format.  So I'm not sure if this is an issue with the way the NIfTI header is read when importing the file into Seg3D2 or how the files are written by Seg3D2.

I have attached a few files to help convey the issues I have encountered. As explained above, all of these files show up correctly in Seg3D2, 3DSlicer, and FSLView, except for file #3 that doesn't show up correctly in FSLView.
  1. thalamusLeft.nii.gz - Segmentation of left thalamus done in FSLView.
  2. thalamusLeft_exportFromSeg3d2.nrrd - Imported file #1 (thalamusLeft.nii.gz) into Seg3d2 and exported as NRRD format.
  3. thalamusLeft_exportFromSeg3d2_exportFromSlicer.nii.gz - Imported file #2 (thalamusLeft_exportFromSeg3d2.nrrd) into 3DSlicer and exported as NIfTI format.
  4. thalamusLeft_exportFromSlicer.nii.gz - Imported file #1 (thalamusLeft.nii.gz) into 3DSlicer and exported as NIfTI format.

Thanks for your help!!


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