Thanks! I'll try that!
Andreia
Citando Nick Schmansky <ni...@nmr.mgh.harvard.edu>:
> you can try:
>
> -talairach -use-mritotal
>
> which will use an alternate talarairch alignment scheme (from the MNI).
> it sometimes works better.
>
> you should also probably add:
>
> -nuintensitycor-3T
>
> to the end of your recon-all command, which will run the nu_correct
> stage optimized for 3T. it wont help you with your talairach issue, but
> people have found that it produces better results for 3T data (versus
> the default nu_correct parameters, which are optimized for 1.5T).
>
> n.
>
>
> On Mon, 2011-10-03 at 15:53 +0100, _andre...@sapo.pt wrote:
>> 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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>> >>> it is
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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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>> >> 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
>> >
>> > _______________________________________________
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>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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