Hi Roberta
we compute but do not apply the talairach transform, so all the volumes,
surfaces, ROIs are in subject space, not talairach.
cheers
Bruce
On Mon, 13 Oct 2014,
Roberta Santoro wrote:
Dear list,
I am new to Freesurfer and I have a doubt about the Talairach
transformation. As
I looked at the nifti files in freeview. The orientation in freeview is
correct, but it appears all of the T1s that resulted in an error are washed out
in freeview. I can vaguely see the outline of the head, but there's a gray box
covering the image. When I click on regions of bone or brain in t
It could be that SPM is setting some scaling factor in the nifti header
that FS is not reading properly. Which version of FS are you using?
doug
On 12/17/2013 02:38 PM, JARED NIELSEN wrote:
> I looked at the nifti files in freeview. The orientation in freeview is
> correct, but it appears all
Hi Bruce,
Thanks for your response. It's a bit of a pain to access the dicoms, but it's
possible. The bigger problem now is that I can't get freeview to work. I type
in freeview into the command line and receive the following error:
freeview.bin: error while loading shared libraries: libvtkverd
Hi Jared
for the ones that run quickly and end, it's because you haven't told it
to do anything. The first couple of lines of the recon-all.log file give
the command line as:
Thu Dec 5 14:00:18 MST 2013
/mnt/NAS3/freesurfer/freesurfer//bin/recon-all
-i Time3_28908_s11038064-0005-1-01-0
I have total of 46 subjects with pre and post scans44 subjects were OK
>>> using the stable version.
>>>
>>> Catherine
>>>
>>>
>>> From: Bruce Fischl
>>> To: Rongxiang Tang
>>> Cc: Nick Schmansky ; Zeke Kaufman
>
-Ubuntu SMP Sat Oct 16 17:39:04 UTC
>> > 2010 i686 GNU/Linux
>> >
>> > recon-all -s 1452 exited with ERRORS at Tue Feb 19 03:31:25 EST 2013
>> >
>> > Thanks,
>> > Catherine
>> >
>> >
>> > __
urfer@nmr.mgh.harvard.edu"
Sent: Thursday, February 14, 2013 2:42 PM
Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
probably not, although it's hard to say. If you upload the whole subject dir
I'll take a look. How does the aseg look?
On Thu, 14 Feb 2013,
trol points to solve the
> problem.
>
> Thanks,
> Catherine
>
> *From:* Bruce Fischl
> *To:* Rongxiang Tang
> *Sent:* Thursday, February 14, 2013 2:03 PM
> *Subject:* Re: [Freesurfer] talaira
Fischl
To: Rongxiang Tang
Sent: Thursday, February 14, 2013 2:03 PM
Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
Hi Catherine
that looks like something went wrong in the surface recon, not in the
talairaching. Maybe a skullstrip problem? You need to investigate. Al
Hi Catherine
can you send us an image of what you are looking at?
thanks
Bruce
On Thu, 14 Feb 2013,
Rongxiang Tang wrote:
Dear All,
When I was checking the talairach transformation output, I noticed that some of
the white matter was not included inside
the green line. Instead of drawing th
t; 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
ia Felber"
> > To: "Avi Snyder"
> > Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\"
> > ,
> > freesurfer@nmr.mgh.harvard.edu
> > Sent: Thursday, September 15, 2011 10:46:55 AM
> > Subject: Re: [Freesurfer] Tala
e, "Avi
Snyder"
Cc: "Bruce Fischl"
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 imag
ain,
> Maria
>
> - Original Message -
> From: "Bruce Fischl"
> To: "Maria Felber"
> Cc: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, September 9, 2011 2:13:05 PM
> Subject: Re: [Freesurfer] Talairach transformation
>
> Hi Maria
>
&
talairach coords are kind of important for
later comparisons.
Thanks again,
Maria
- Original Message -
From: "Bruce Fischl"
To: "Maria Felber"
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
16.3635120391846
Yi-Yu
From: Nick Schmansky [ni...@nmr.mgh.harvard.edu]
Sent: Tuesday, June 14, 2011 11:14 AM
To: Bruce Fischl
Cc: Yiyu Chou; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1
a change in 5.1 over
a change in 5.1 over 5.0 is that in 5.1 the talairach stage takes
orig.mgz as input, whereas in 5.0 and prior, it used nu.mgz as input.
(this was done so that the nu correction stage could make use of the
talairach.xfm).
you can either:
- add the flag -use-mritotal to the end of recon-all to hav
is this the talairach.xfm?
On Tue, 14 Jun 2011, Yiyu Chou wrote:
> Dear Freesurfer users,
>
> I got different transformation matrices (shown below) when running ver 5.0
> and ver 5.1 on the same subject
> - ver 5.0 was doing great but ver 5.1 failed:
> I would appreciate it if you can give me som
Hi Thomas,
have you visually inspected the talairach.xfm file? This error means that
the parameters of the transform fall far enough outside the normal range
that it is suspicious. You can rerun with -notal-check if you are sure it
is correct, but you should check and possibly fix it.
cheers
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