Hi Uri,

is there some other problem? I suspect that if you displayed the nifti in tkmedit it would look the same. We center the coords and reslice to coronal to display things in a standard location/orientation.

cheers Bruce

On Sat, 10 Nov 2012, Uri Hasson wrote:

Dear Freesurfer experts,

I'm converting a batch of nifti files to start a FS pipeline. There is 1 structural image per participant. The initial 'reconall -i' step does not give any errors. But, looking at the 'mri/orig/001.mgz' I notice for 1 participant what appears to be an imperfect conversion.

Here is the link to the image showing this small bug.. http://goo.gl/jJKgM

It shows the same coronal slice in AFNI and FS. The one on the right is how the original brain looks in AFNI, the one on the left is the FS's 001.gmz where there appears to be a 'pixel shift both saggitally and axially..

Any assistance, much appreciated. Thanks, Uri _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer