You can use this version of mris_apply_reg https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg Something like mris_apply_reg --src-xyz lh.white --lta rawavg.lta lh.white.rawavg Where rawavg.lta is created with tkregister2_cmdl --mov orig.mgz --targ rawavg.mgz --regheader --reg deleteme.dat --ltaout rawavg.lta

On 3/12/19 1:22 PM, Peled, Noam wrote:

Hey Bruce. Originally this is what I did. I used mri_convert on the relevant nii files, but I was wondering what to do with the surfaces files. I thought it'll be easier to create all of these files directly in RAS orientation.

Thanks, Noam

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Friday, March 8, 2019 11:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Sophie Esterer EstererS@cardiff.ac.uk Subject: Re: [Freesurfer] recon-all: making sure that brain.mgz will be in RAS orientation.

Hi Noam

if you want your outputs in a specific coordinate system, why not just run recon-all, then mri_conver to whatever orientation you want? Internally we have a consistent orientation that you can't easily change

cheers Bruce On Sat, 9 Mar 2019, Peled, Noam wrote:

...

Dear group, I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz turn out to be in LIA orientation. I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS --out_orientation RAS ...), and rerun recon-all, but it didn't change the results. How do I make sure my output files will be in RAS orientation?

Thanks, Noam

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