you could also try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI).
it sometimes works better (not necessary for 3T).
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
will produce better results for 3T data downstream.
n.
On Wed, 2011-09-28 at 16:38 -0400, Bruce Fischl wrote:
> 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
> >>> it is
> >>> addressed. If you believe this e-mail was sent to you in error and the
> >>> e-mail
> >>> contains patient information, please contact the Partners Compliance
> >>> HelpLine at
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> >>> in error
> >>> but does not contain patient information, please contact the sender and
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> >>> dispose of the e-mail.
> >>>
> >>>
> >>>
> >>
> >> --
> >> 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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