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