Sarah,

You can use the -motioncor option of recon-all to perform the averaging. Refer to:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

Notice this assumes that the input files are already in the <subject>/mri/orig directory. To do this, given two structural dicoms:

recon-all -s <subjid> \ -i /path/to/dicoms/12345_1.dcm -i /path/to/dicoms/12345_2.dcm -motioncor

Here, 12345_1.dcm is one file (an example filename) from the first structural (the filenames of the slices will be automatically determined), and 12345_2.dcm is the other structural.

Note that after the 001.mgz and 002.mgz files are created, the -i option is no longer necessary to include with recon-all.

Nick

On Mon, 2007-10-01 at 14:51 -0400, Sarah J Greene wrote:

Hi all, I have a question about averaging scans. We are trying to average 2 scans taken one after another on the same person to run them through FreeSurfer, but are not sure of the command to do this. Does anyone know of the command, and at what point in processing to use it? Thanks! sarah _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer