Re: [Freesurfer] mri_convert and image orientation

not necessarily. For FSL, the determinant must be less than 0 (see mri_info output). Having said that, even if the det<0, it may still show up funny in fslview

On 01/25/2016 12:11 PM, Yang, Daniel wrote:

Dear FreeSurfer experts,

I find that mri_convert will convert DICOM of structural scan to neurological orientation by default.

For example, mri_convert --in_type dicom --out_type mii <first file in the DICOM directory> <output.nii.gz>

Thus, the NII may need to be swapped in x for use in FSL.

In this the case?

Many thanks, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu

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