Hong,

If you add -help to recon-all, it has a section on longitudinal processing. longitudinal processing assumes your timepoint 1 subject has already been processed by the normal stream (ie, recon-all -all -s <subjid>). That will produce the files you mention.

However, we have recently made significant improvements in the longitudinal stream, which will appear in the next stable release. If you want to work with those updates, you can get them for centos4 here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/centos4

copy them to your $FREESURFER_HOME/bin.

You will still need to process your tp1 subject by the normal-stream (and also the longitudinal stream).

Nick

On Mon, 2008-09-08 at 09:02 -0400, Xie, Hong wrote:

Hello, group,

I am running longitudinal process step by step following the wiki

page of 12 differences between longitudinal and recon-all process. But some needed files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz, wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fill.mgz, brain.finalsurfers.mgz, ?h.smoothwm, ?h.inflated, ?h.sulc, and ?h.aparc.annot. Should I use recon-all commands to create these files or just copy ( or transform) them from tp1 to tp2? Thank you for help.

Hong

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