I am using a GE 3T scanner with a slice thickness of 1.7 mm. I tried using the new script you provided (thanks for the help!) and it did not seem to make any difference with the couple of subjects that I tried. I have attached a screenshot. The right image in the screenshot is the original Talairaching and the left is after I ran the script you provided. Does this mean I will be forced into manually editing the Talairach for all of my subjects and re-running recon-all for all of them after I do that or is there another solution?

Peter

Message: 4
Date: Tue, 11 Jun 2013 13:41:47 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: Talairach Positioning in Horizontal
        View
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <51B7615B.7000606@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Peter, what scanner are you using? You might be better off with using
a 3T atlas. Spec -schwartzya3t-atlas with recon-all and see if that
cleans it up. You can run just the talairaching with

recon-all -s subject -schwartzya3t-atlas -talairach

doug



On 06/11/2013 01:03 PM, Peter Boulos wrote:
> I am very new to the software and have just begun assessing Talairach
> outputs for my subjects. I am confused in that I cannot seem to find a
> balance I am happy with between positioning of the green lines in both
> the horizontal and sagittal views for multiple subjects. I opened the
> talairach output with the following command (tkregister2 --mgz --s
> SUBJID --fstal --surf orig) and everything looked perfectly aligned
> for all the subjects I have tried in both the coronal and sagittal
> views but in the horizontal view the green lines went well off the
> back of the brain. I have attached a screenshot. I tried to translate
> the brain but that did not seem to solve my issue and I realized I
> needed to scale the length of the brain. When I did that I was more
> pleased with the outcome but the corpus callosum did not match up
> nearly as well after I did that (second attached screenshot) and that
> was the primary landmark I was using to pass my images in terms of
> talairach output assessment. Do you have any advice for me?
>
> Peter
>
>
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