help > RE: Some questions about the Dicom2nii.exe
Oct 9, 2019  04:10 AM | Chris Rorden
RE: Some questions about the Dicom2nii.exe
Can I suggest you upgrade to 2019 versions of MRIcron or MRIcroGL? These will include the modern dcm2niix rather than the older dcm2nii. While I hope my old tools are robust and mature, the vendors are constantly updating their DICOM images (e.g. moving to enhanced DICOM). You can either use dcm2niix from the command line, or use the MRIcron/MRIcroGL "Import" menu for a graphical interface. dcm2niix will always rotate 3D images to the nearest orthogonal rotation to a NIfTI identity matrix (hence, no 'o' images), but does provide the option to crop 3D images. Cropping attempts to remove excess neck from T1-weigthed MRI scans of the brain. Excess neck can disrupt some tools such as SPM8 and FSL's BET. The newer normalization in SPM12 appears very robust against this. If you are only interested in the brain, the cropped images will require less disk space, lead to more robust processing, and process faster. On the other hand, if you are interested in other body parts, or if the neck is of interest, you will want to preserve it.

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peilunsong peilunsong Oct 9, 2019
RE: Some questions about the Dicom2nii.exe
Chris Rorden Oct 9, 2019
peilunsong peilunsong Oct 9, 2019
Chris Rorden Oct 9, 2019
peilunsong peilunsong Oct 9, 2019
Chris Rorden Oct 10, 2019