questions > How keep oringinal slice order
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Dec 13, 2019  06:12 AM | Haifang Li - Stony Brook University
How keep oringinal slice order
Hi Exports,

I have a sagittal dicom series with 192 of 512x512 image.
The older dcm2niigui generats a nii file with dimension of 512x512x192 and newer (2019) dcm2niix generates a nii file with 192x512x512.
Is there any option in dcm2niix to generate same nii file as dcm2niigui.

Thanks,

Haifang Li
Dec 13, 2019  07:12 AM | Chris Rorden
RE: How keep oringinal slice order
dcm2niix will rotate 3D acquisitions to be roughly aligned with canonical NIfTI space. You can disable this by adding the argument '-x I'. Note this rotation is only applied to 3D volumes, so unlike 2D EPI sequences the original slice order does not reflect the temporal order of acquisition.


Chris Rorden's dcm2niiX version v1.0.20191206 Clang11.0.0 (64-bit MacOS)
usage: dcm2niix [options]
Options :
-1..-9 : gz compression level (1=fastest..9=smallest, default 6)
...
-x : crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquistions)
....