Hi Hakon,
I have not yet tried this, but I would recommend (see below):
On Mon, 2009-10-12 at 17:10 +0200, hakon.grydeland@psykologi.uio.no wrote:
Hi,
I have a couple of questions regarding manual edits such as deleting non-brain tissue included in the pial surface in the longitudinal stream (v4.5):
- Where in the longitudinal stream would you recommend doing edits? On
the brainmask.mgz of the base?
Yes, fix it in the base, because the brainmask.mgz is mapped from the base to all timepoints and used in the -long stream.
- If so, would you then re-run the base as a cross-sectional (recon-all
-s baseid -autorecon2-pial -autorecon3)?
No, there are differences in the base from the regular cross-sectional stream (e.g. gcareg and canorm are different). Therefore you need to rerun the base stream from that location. I have never tried this, but do not see a reason why it should not work.
Good luck, Martin.
Thanks,
Håkon
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