Re: [Freesurfer] recon-all

On 11/04/2015 10:22 AM, John Anderson wrote:

Hi freesurfers, Following recon-all I have a collection of folders inside the subject folder. Inside the folder "mri" I have collection of files:

1. What is the differnce between the file "orig.mgz" and the file

"norm.mgz" ?

norm has been skull stripped and intensity normalized

2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel

dimentions are equal while in orig.mgz it is not)?

They should be the same. It might be differnt than rawavg.mgz or your input data because we "conform" all inputs to 256^3 1mm3

3. Is it correct if I convert norm.mgz to "nii" file and use it as a

"T1" for further processing?

I don't know without knowing more about the "further processing". It is not a T1 image itself (ie, the voxel intensities are not T1 in msec).

bests, John Anderson

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer