I wonder whether there is a way to convert surfaces back to the subject
native space. Thanks!
Anqi Qiu
Center for Imaging Science
The Johns Hopkins University
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Today's Topics:
1. Re: tkregister2:views mixed up. (Chacko Cherian)
2. Re: tkregister2:views mixed up. (Doug Greve)
3. Re: brainmask.mgz problems (Bruce Fischl)
4. error with mri_ca_register (Binyam Nardos)
----------------------------------------------------------------------
Message: 1
Date: Mon, 5 Feb 2007 15:47:55 -0800 (PST)
From: Chacko Cherian <chacko_cherian@yahoo.com>
Subject: Re: [Freesurfer] tkregister2:views mixed up.
To: Doug Greve <greve@nmr.mgh.harvard.edu>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <570151.930.qm@web35315.mail.mud.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Yes,It is perfectly fine with the --regheader optionmwhich means no problem
with geometry info.
But how do I fix the talairach.xfm?
Thanks a lot!
Chacko.
--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
I mean to just load the orig.mgz into tkmedit and see if it is
oriented correctly. Assuming that it is oriented correctly, then it
sounds like the talairach transform is messed up pretty badly.
When you run
tkregister2, try adding --regheader. This will ignore the info in the
talairaach.xfm file and force it to use the geometry info. it will
likely be very far off, but the basic orientation should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the transform..i checked
brainmask.img and T1.img after loading the transform and they had
this
problem..The
header and geometry info look fine..
--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
That means that the geometry info in the file is messed up. Where
did the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
Hello ALL,
Has anybody had trouble with tkregister2..I
loaded
the
transform and the coronal and horizontal views
are
mixed up.Coronal view of the subject is coupled
with
the horizontal view of the talairach volume.
Thanks in advance
Regards,
Chacko.
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greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
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Message: 2
Date: Mon, 05 Feb 2007 20:20:04 -0500
From: Doug Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] tkregister2:views mixed up.
To: Chacko Cherian <chacko_cherian@yahoo.com>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <45C7D7C4.2070908@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
You can start with that one and fix it by hand (which is a hassle). We are
working on ways to make the talairach more robust. BTW, if you run
tkregister2 again after fixing it, you should not include the --regheader as
that will ignore your previous edits.
doug
Chacko Cherian wrote:
Yes,It is perfectly fine with the --regheader optionmwhich means no
problem with geometry info.
But how do I fix the talairach.xfm?
Thanks a lot!
Chacko.
--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
I mean to just load the orig.mgz into tkmedit and see if it is
oriented correctly. Assuming that it is oriented correctly, then it
sounds like the talairach transform is messed up pretty badly.
When you run
tkregister2, try adding --regheader. This will ignore the info in the
talairaach.xfm file and force it to use the geometry info. it will
likely be very far off, but the basic orientation should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the transform..i checked
brainmask.img and T1.img after loading the transform and they had
this
problem..The
header and geometry info look fine..
--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
That means that the geometry info in the file is messed up. Where
did the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
Hello ALL,
Has anybody had trouble with tkregister2..I
loaded
the
transform and the coronal and horizontal views
are
mixed up.Coronal view of the subject is coupled
with
the horizontal view of the talairach volume.
Thanks in advance
Regards,
Chacko.
____________________________________________________________________
________________
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Check out "Tonight's Picks" on Yahoo! TV.
http://tv.yahoo.com/
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Message: 3
Date: Mon, 5 Feb 2007 21:58:56 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] brainmask.mgz problems
To: Catherine Hartley <cate@nyu.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<Pine.LNX.4.62.0702052157510.24903@gate.nmr.mgh.harvard.edu>
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Hi Cate,
there is a section on the wiki about troubleshooting the skullstripping.
Try some of those recommendations first (mostly changing the preflooding
height). If the cerebellum is messed up, then the aseg probably won't work
well which can hurt the whole processing stream.
cheers,
Bruce
On Mon, 5 Feb 2007, Catherine Hartley wrote:
Hi,
I ran autorecon1 on a group of data consisting of a single set of
mprage DICOMs per subject, acquired on a Siemens Allegra 3T scanner.
Several of the brainmask.mgz images had large portions of the
brainstem and cerebellum removed. A couple had portions of the neck
which were not removed. The talairach transforms looked fine.
A more experiened Freesurfer user suggested that adding control points
and re-running the intensity normalization might fix this. I assume
that I can follow the instructions here,
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fControlPoints
but that I would need to edit the orig.mgz file and then run
autorecon1-cp.
Is this correct?
My intended analysis (cortical thickness in PFC regions) does not
depend upon these flawed regions, but I want to make sure these errors
aren't indicative of some larger problem. Also, I know there have
been issues with gradient warping with the Allegra. Do these problems
sound like gradient warping symptoms?
Thanks,
Cate
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------------------------------
Message: 4
Date: Tue, 6 Feb 2007 10:39:23 -0600
From: "Binyam Nardos" <binyamn@npg.wustl.edu>
Subject: [Freesurfer] error with mri_ca_register
To: <Freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<D137A6563A0D774583072D87B777269E0152B4A3@nilex01.neuroimage.wustl.edu>
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