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
>>>
>>>
>>
>>
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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
>
>_______________________________________________
>Freesurfer mailing list
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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
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