Hi Louis,

Thanks again for your help! In addition, I was wondering: Would it be ok to follow the exact same procedure/pipeline (that is the mri_robust template command, followed by the mri_convert and mri_add_xform_to_header commands) if I only have one movable volume (for the mri_robust_template command), or do I need to just run only the mri_convert and mri_add_xform_to_header commands if I have one volume as the input ? Thank you for your time.

Best, Panos ________________________________________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 1:00 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Motion correction in recon-all

Hi Panos, The motion correction itself is carried out using the mri_robust_template binary. The motion correction step also includes an mri_convert command to conform the volume and mri_add_xform_to_header.

example taken from recon-all dev table: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta

-Louis

On Mon, 15 Jul 2013, Fotiadis, Panagiotis wrote:

Hi FS Community,

I was wondering which command(s) is(are) being used in the "Motion Correction" part of the recon-all process, to merge the mri/orig/XXX.mgz files and correct for any motion. Thank you for your time!

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