the first command you show is what you should use (all flags on one
line).
permanent changes are listed here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits
note that since you have run talairach once already, it will keep that
prior run, so you will also want to include -clean-tal at the end of
your recon-all command.
n.
On Thu, 2011-10-06 at 13:22 +0200, Maria Felber wrote:
> Dear Nick,
>
> how do I best implement your suggestions in my command line?
>
> e.g. recon-all -all -use-mritotal -nuintensitycor-3T -s im30 or
>
> recon-all -motioncor -s im30
> recon-all -talairach -use-mritotal -s im30
> recon-all -all -nuintensitycor-3T -s im30
>
> As I have not a clue what changes will be saved by freesurfer or wethere they
> are just overwritten by a new command, please advise have best to follow you
> advise. Thank you.
> Sincerely,
> Maria
>
> ----- Original Message -----
> From: "Nick Schmansky" <ni...@nmr.mgh.harvard.edu>
> To: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> Cc: "Maria Felber" <fel...@cbs.mpg.de>, s...@nmr.mgh.harvard.edu,
> freesurfer@nmr.mgh.harvard.edu
> Sent: Wednesday, September 28, 2011 10:53:08 PM
> Subject: Re: [Freesurfer] Fwd: Talairach transformation
>
> 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
> > >>> http://www.partners.org/complianceline . If the e-mail was sent to you
> > >>> in error
> > >>> but does not contain patient information, please contact the sender and
> > >>> properly
> > >>> 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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> > >
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