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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