Hi Nikhil,

If you are only interested in the norm.mgz you don't need the longitudinal pipeline, because that is designed to give you more reliable segmentations and surfaces.

Simply run 1 and 2 and you have the norm for all subjects / time points. If you want to register them into the same space within each subject, do it manually with mri_robust_template after they are created.

Best, Martin

On 08/29/2013 05:54 AM, Nikhil Pratap Singh wrote:

Hi ,

I am new to longitudinal processing using freesurfer. I am about to process a big dataset of longitudinal images.

If in the end, I am only interested in norm.mgz file, is there a way I can speed up the processing time of the entire pipeline?

Since norm.mgz gets created in cross sectional processing after canorm steps of autorecon2, would these sequence of commands work for a subject?

1. recon-all -autorecon1 -subjid <tpNid>
2. recon-all -autorecon2 -subjid <tpNid> -gcareg -canorm
3. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all
4. recon-all -long <tpNid> <templateid> -all

Thanks in advance, Nikhil

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