Hi all,
I have the same problem. I'm also working with 3T, and I need to
stretch the movable template with tkregister2 in almost every subject.
It would be nice if this wasn't necessary, is there a workaround?
Thanks,
Andreia
Citando Maria Felber <fel...@cbs.mpg.de>:
> 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
>>>>
>>>>
>>>
>>>
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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
>> Freesurfer@nmr.mgh.harvard.edu
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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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