You need something like this

mri_vol2vol --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o fsaverage.orig.MNI152.nii.gz --inv --reg $SUBJECTS_DIR/fsaverage/mri/transforms/reg.mni152.2mm.dat

On 04/03/2017 10:36 AM, Melanie Ganz wrote:

Hi all,

my colleague Vincent wanted to register a volume in MNI305 to MNI152, unfortunately the final image appears flipped up-down and anterior-posterior when using the --mni152reg flag with mri_vol2vol. For example, trying to resample fsaverage orig.mgz to MNI152 using

mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mni152reg --o fsaverage.orig.MNI152.nii.gz

ends up yielding the attached image (red is the output file and background is FSL MNI152 template). Anything obvious he's doing wrong?

Cheers,

Melanie

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