The orig.mgz is closer to the raw data than T1.mgz, but it will be different in a number of ways. First, it will be 256^3, 1mm voxel size regardless of the dimensions of the raw data. Second, it will be 8 bits (0-255) with some rescaling.

On 5/2/18 7:43 AM, C.P.E. Rollins wrote:

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Just to clarify, by that I mean would the NIFTI converted from orig.mgz (with mri_convert) be different than the NIFTI produced by dcm2niix from the raw DICOMs?

Thanks, Colleen

-------- Original Message -------- Subject: orig.mgz versus T1.mgz Date: 2018-05-02 10:24 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu

Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way?

Thanks again, Colleen

-------- Original Message -------- Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu

Dear Freesurfer developers,

A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 NIFTI files.

Many thanks, Colleen

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