Hi Maria
have you tried running without the talairach stuff? Try -notalairach and
see if it works for you
cheers
Bruce
On Wed, 28 Sep 2011, Maria Felber wrote:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to
everyone so far troubled with my question, I am trying here for a second time.
It is indeed the case, that all my data were scanned with a 3T. And if that is
indeed the problem Dr. Snyder figured out, then what can I do about it? Or is
anyone already working on this problem? I can hardly imagine I am the only one
recording with a 3T instead of a 1.5T.
Yours sincerely,
Maria Felber
----- Forwarded Message -----
From: "Maria Felber" <fel...@cbs.mpg.de>
To: "Avi Snyder" <a...@npg.wustl.edu>
Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\" <a...@npg.wustl.edu, Bruce
Fischl" <s...@nmr.mgh.harvard.edu>, freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, September 15, 2011 10:46:55 AM
Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about
it or do you have something in progress which would fix this problem anytime
soon?
Thanks,
Maria
----- Original Message -----
From: "Avi Snyder" <a...@npg.wustl.edu>
To: "Sita Kakunoori" <s...@nmr.mgh.harvard.edu>, fel...@cbs.mpg.de, "Avi Snyder"
<a...@npg.wustl.edu>
Cc: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
Sent: Tuesday, September 13, 2011 11:03:28 PM
Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are
expected if the contrast properties of the sample image are far from those
of the target. This condition can easily occur if the target is based on
1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images
tend to be relatively bright in the center of the head.) Gd++ contrasted
MP-RAGE scans routinely do not produce decent atlas transforms unless
special measures are taken. A FreeSurfer fix for this problem is
theoretically feasible.
Avi
-----------------------------------------------
On 9/13/11 2:26 PM, "Sita Kakunoori" <s...@nmr.mgh.harvard.edu> wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this
e-mail.
Hi Dr.Snyder, Not sure if you remember but we saw something similar in a
dataset here at the center where the talairach was much smaller than the
orig.mgz volume and you created a new talairach template to be used with
that dataset. I just wondered if this issue is similar to that.
Thanks much,
Sita.
---------- Forwarded message ----------
Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST)
From: Maria Felber <fel...@cbs.mpg.de>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did
exactly that and checked the xform using tkregister2. And here I always
see that my talairach volume (the transform) is always smaller, which can
be very well seen as the orig surfaces of the subjects are always a
little outside the brain and reach well into the skull areas. Of course I
can make the adjustments as descriped in the short instructions. But this
also means I ran the recon-all precess anew for another 30 h per subject.
And that is the reason, why I asked if this is normal that the tailarach
transform is a) always smaller than the original brain, and b) if I can
make any adjustments to prevent that from happening and thus saving
another 30h per subject.
In short: How acurate hat the talairach.xfm has to be and is it possible
to change some parameters to make this transformation a little more
accurate while running the recon-all process only once?
Best,
Maria
----- Original Message -----
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Maria Felber" <fel...@cbs.mpg.de>
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, September 13, 2011 4:07:55 PM
Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm
transform ("xform" for short), and correct it if you want.
cheers
Bruce
On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the
webpage about xform, but failed. So what is xform standing for and
where/how can I check it?
As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind
of
important for later comparisons.
Thanks again,
Maria
----- Original Message -----
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Maria Felber" <fel...@cbs.mpg.de>
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, September 9, 2011 2:13:05 PM
Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless
for some reason you care a lot about the accuracy of the talairach
coords.
cheers
Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I
simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the
recon-all -all process. The process finished without errors. So the
next step was to check the talairach transform.
Now, according to the FsTutorial/Talairach I have to make some
adjustments and then run the whole process again. That is all nice and
good.
However, why is it, that the talairach volume is always, no matter
which subject I look at, is always significantly smaller than the
target volume? Is that normal? Has it to be fixed? Or is that just
normal? Attached find one example.
As I am using freesurfer for the first time, I am really unsure about
that.
Thanks for the help,
Maria
The information in this e-mail is intended only for the person to whom
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--
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A
04103 Leipzig, Germany
Phone: +49 341 9940-2465/2522
--
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A
04103 Leipzig, Germany
Phone: +49 341 9940-2465/2522
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