How do you know the nifti files are correctly oriented to begin with? doug On 10/24/2013 07:07 PM, Chiu, Bryan (PHTH) wrote:

Hi,

I am working on a dataset using free surfer.

I have NIFTII files which I am converting using mri_convert. Upon completion of mri_convert, the orientations of the files are wrong. This likely leads to an incorrect talairach (I was getting errors but used -notal-check) and leads to an incorrect labelling of volumes from the -autorecon-all.

My sagittal view is rotated 90 degrees clockwise on the MRI convert. The sagittal and coronal views are swapped. This appears in a tkmedit of the converted file.

error codes during mri_convert are as follows:

$ mri_convert '/Applications/freesurfer/subjects/001test/xxxxx-file-xxxxxx.nii.gz' '/Applications/freesurfer/subjects/001test/''orig2.mgz' mri_convert /Applications/freesurfer/subjects/001test/xxxxx-file-xxxxxx.nii.gz.nii.gz /Applications/freesurfer/subjects/001test/orig2.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/001test/HANDY_POWER_001_10_1_NIFTI.nii.gz... WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/001test/orig2.mgz

guidance to fix this would be appreciated.

• Bryan

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