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