Hi Bruce,
Thank you for your suggestions. I just finished the -autorecon1 step with v4.0.1 for 20 subjects, and checked the talairach registration with tkregister2. I found that most subjects' talairach volume looked smaller than the T1 volume. Suppose this is a "not very good" talairach registration, my questions are:
1. Is a "good" talairach registration critical to the further recon-all steps? 2. If yes, can I use the talairach transformation file generated after I manually modified the talairach registration with v3.05 for the same subject?
Thanks for your helps,
Xiangchuan
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Date: 2007-09-17 Time: 18:28:46 From: Bruce Fischl (fischl@nmr.mgh.harvard.edu) To: Xiangchuan Chen (xiangchuan.chen@bme.emory.edu) Subject: Re: [Freesurfer] re-run FreeSurfer with v4
Hi Xiangchuan
Avi Snyder's new talairach doesn't seem to fail anymore, and the skullstrip failures are now extremely rate, so you might just let the whole thing chug through and only check it at the end to make sure the surfaces are accurate.
cheers, Bruce
On Mon, 17 Sep 2007, Xiangchuan Chen wrote:
Hi all,
I am working on 80 subjects' data with the following work flow:
- -autorecon1
- edit talairach registration
- -autorecon1
- -autorecon2
- edit brainmask.mgz
- edit wm.mgz
- -autorecon2-wm
- -autorecon3
I have already finished this work flow for 30 subjects with FreeSurfer v3.05. I have spent a lot of time on steps 2, 5 and 6. I am not worrying about the other steps because they are my computer's tasks, but not mine. So, if I re-run the same work flow with v4, do I have to go through all these steps?
Any suggestions are greatly appreciated.
Thanks in advance,
Xiangchuan Chen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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