Thanks Allison,

So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that?

Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch?

Thanks so much for looking into this for me!

Best,

Krista

On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens <astevens@nmr.mgh.harvard.edu> wrote:

Hi Krista,
I took a look at your subject and think I have determined the problem. Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the talairach registration step failed. If you look at the talairach.xfm, you'll see it is way off:
tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig

But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm to talairach.xfm and rerun from the -normalization step.

You might also want to look at these instructions:
https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon

They might not all apply to you but could potentially.
Allison

---------- Forwarded message ----------
Date: Thu, 03 Oct 13 22:55:12 -0400
From: krista.kelly16@gmail.com
To: fischl@nmr.mgh.harvard.edu
Subject: V1 Labels

Hey!

Krista  (krista.kelly16@gmail.com) has uploaded some files for you at the Martinos Center FileDrop:

-> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4>

Also, they left this message for you:
Hi Bruce,

Here is a zipped file of one of the subjects that I'm having label troubles with. The lh.v1.label isn't mapping correctly. I find the same goes for the aparc atlas as well (I haven't checked out anything else). If you could help me figure out why this is happening, that would be great!

Thanks,
Krista

Please be aware, your upload will expire on December 31st. If you'd like to download these files, feel free to use the link below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf

Cheers,
The NMR Team

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