Hi Doug thank you for the quick response!

The source is a Siemens scanner. Data derived from the Spine. I don't know what is the optimal way to convert these ima images to nifti

what is the source of the ima file? was it anonymized? You can try something like adding

-iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1

but this is just guessing at the orientation

-------- Original Message -------- Subject: mri_convert Local Time: May 15, 2017 9:58 PM UTC Time: May 16, 2017 1:58 AM From: John.anderso@protonmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu

Dear Freessurfer experts, i want to convert IMA files to nifti using mri_convert I did the following:

mri_convert 54365413.ima output.nii

I got this error WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER!

How can I correctly convert IMA to nifti Thank you for any suggestion John