That is just the failure detection. Sometimes it generates a false positive.
Did you check the transform? If the rest of the downstream processes (eg, aseg
and surfaces) are ok, then you don't need to worrry
On 12/21/2020 6:53 PM, Wei Shao wrote:
External Email - Use Caution
Hi, Freesu
External Email - Use Caution
Hi, Freesurfer team
I have met a Talairach Failure problem when running the recon -all for a
subject, here is the feedback: I tried -notal-check flag, but it might
cause another problem when I use segmentHA_T2.sh to do hippocampus subfield
segmentation
Hello all,
I have 2 subjects that failed autorecon-all at the same Talairach step.
Both subjects successfully completed autorecon-all in version 5.2. Here is
the output from one of the subjects.
Any suggestions?
Corinna
#
#@# Talairach Fri Feb 28 12:39
Thanks a lot!,Pablo
Date: Fri, 30 Aug 2013 11:38:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: pablon...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
yes, any single file that is in the correct series should be fine
Bruce
On Fri
on...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 27 Aug 2013 17:14:04 +
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips
format. Would you recommend to convert to DICOM anyway? Or should I used
NIFTI?Than
place of "nii.gz" file? Can
> I use any of the MR.1.3.12.2 (listed above)?
> Many thanks,
> Pablo
> ----
> From: pablon...@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Tue, 27 Aug 2013 17:14:04 +
&g
I use any of the MR.1.3.12.2
(listed above)? Many thanks,PabloFrom: pablon...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 27 Aug 2013 17:14:04 +
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philip
From: pablon...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 27 Aug 2013 17:14:04 +
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips
analyze format. Thank you
for your support,Pablo
From: pablon...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 27 Aug 2013 17:14:04 +
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips
format. Would
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best
On Tue, 27 Aug 2013, pablo najt wrote:
> Thank you very much for your input. Yes, I did start with analyze format and
> also I have visually inspected the images. Almost all my
> scans consiste
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed
incorrect? What input format did you start with? Most of these occur
because people start with analyze, which doesn't have the direction
cosines
best is to start with either DICOM or NIFTI and avoid analyze
format. Is this correct?
Best,Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400
From: fis...@nmr.mgh.harvard.edu
To: pablon...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed
incorrect? What input format did you start with? Most of these occur
because people start with analyze, which doesn't have the direction
cosines, and so the data is oriented incorrectly
cheers
Bruce
On Tue, 27
Dear FS experts,I am contacting you to report an error after launching recon
-all for one of my subjects (see below). I am using a macbook pro with snow
leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to
correct this.Thank you for your attent
Dear FS experts,I am contacting you to report an error after launching recon
-all for one of my subjects. I am using a macbook pro with snow leopard version
10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to
correct this.Thank you for your attention,P
Well, in the PACs looks fine. When converting to nii it is already wrapped.
I will go to the machine again and see.
Thanks!
2012/10/30 Bruce Fischl
> really? In what viewer? Does it happen in the rawavg.mgz?
>
>
> On Tue, 30 Oct 2012, Daniel Ferreira wrote:
>
> Hi,
>> I see. But why does it
really? In what viewer? Does it happen in the rawavg.mgz?
On Tue, 30 Oct 2012, Daniel Ferreira wrote:
Hi,
I see. But why does it happen? If I look at the initial Dicom it is normal,
no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl
Hi Daniel
it looks like you hav
Hi,
I see. But why does it happen? If I look at the initial Dicom it is normal,
no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl
> Hi Daniel
>
> it looks like you have too much wrap in your image, with a significant
> amount of brain wrapping to the top. Nothing will work on t
Hi Daniel
it looks like you have too much wrap in your image, with a significant
amount of brain wrapping to the top. Nothing will work on this
sorry
Bruce
On Tue, 23 Oct 2012, Daniel Ferreira
wrote:
Hi Nick,
Here comes attached the tkmedit orig.mgz
thanks
Daniel
2012/10/22 Nick Sch
what does orig.mgz look like in tkmedit?
n.
On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote:
> Hi,
>
>
> I did recon-all -i -s
>
>
> and then what Nick posted.
>
>
>
> 2012/10/18 Bruce Fischl
> Hi Daniel
>
> what was your original data format? Did you
Hi,
I did recon-all -i -s
and then what Nick posted.
2012/10/18 Bruce Fischl
> Hi Daniel
>
> what was your original data format? Did you start with dicoms?
> Bruce
>
> On Thu, 18 Oct 2012, Daniel Ferreira wrote:
>
> Thanks Nick very much for your suggestion.
>> Unfortunately it did not fix
Hi Daniel
what was your original data format? Did you start with dicoms?
Bruce
On Thu, 18
Oct 2012, Daniel Ferreira wrote:
Thanks Nick very much for your suggestion.
Unfortunately it did not fix the error.
I run the mri_nu_correct command trying several -n values (1, 5, 20), then I
-talaira
Daniel,
See this page which i just created which describes a workaround to a
problem some people are having with the Talairach stage in the v5.1
release:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
Nick
On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote:
> Dear experts,
>
> Pl
did you check the accuracy of the talairach with tkregister2 or tkmedit?
If it's really bad, then you can either fix it with tkregister2, or tell
recon-all to not use it. If it is accurate but being incorrectly flagged,
you can tell recon-all to skip the checking.
cheers
Bruce
On Wed, 3 Nov 2
Hi Kristina,
You can find the answer to your question here:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F
As a new user, you might find that FAQ helpful.
Allison
--
On Wed, 3 Nov 2010, Rapuano, Kristina (N
Hello there,
I am fairly new to freesurfer, and received an error message that I am not sure
how to handle. I was running recon-all (-autorecon1 and -autorecon2) which then
quit with this error:
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#
can you get to the data before it got converted to analyze? If not, how
will you ever know left from right?
On Mon, 10 May 2010, Antoine Leflon
wrote:
With tkregister2 I've just noticed my problem was that the movable is
not done properly because when I switch on it I see a white screen or
som
With tkregister2 I've just noticed my problem was that the movable is
not done properly because when I switch on it I see a white screen or
something blurred .
any one could help ?
Antoine leflon
Bruce Fischl a
yes, but if the information is lost in analyze (which it is) then we are
just guessing about orientations when we are converting back to .mgz
On Tue,
4 May 2010, Ilana Hairston wrote:
trying to make sense of this:
1. ran the initial recon-all to convert analyze to .mgz
2. then mri_convert on
trying to make sense of this:
1. ran the initial recon-all to convert analyze to .mgz
2. then mri_convert on the DICOMs overwriting 001.mgz.
Now running the full autorecon-all to see what it looks like, but is seems
that mri_convert added spatial cosine information to the 001.mgz. this was
the o
usually you create an mri/orig/001.mgz, but you can also just point
recon-all directly at the dicoms I think
On Tue, 4 May 2010, Antoine Leflon
wrote:
So I have to write : mri_convert -it dicom -i (first image) -o (name
of the file) ?
I did it outputing orig.mgz as usually before getting the e
So I have to write : mri_convert -it dicom -i (first image) -o (name
of the file) ?
I did it outputing orig.mgz as usually before getting the error .
Antoine
Bruce Fischl a écrit :
> mri_convert can be used to ch
there's a tutorial for this on the wiki. It's pretty detailed - let us
know if you have any problems.
cheers
Bruce
On Tue, 4 May 2010, Antoine Leflon wrote:
No I haven't , what is the syntax for this ?
tkregister2 (name) (mgz file) ?
thanks ,
Antoine
No I haven't , what is the syntax for this ?
tkregister2 (name) (mgz file) ?
thanks ,
Antoine
Bruce Fischl a écrit :
> have you visually verified the talairach failed with tkregister2? If you
> bring up the orig.m
mri_convert can be used to change the format, assuming it is standard
dicom.
cheers
Bruce
On Tue, 4 May 2010, Antoine Leflon wrote:
> My files are dicoms and have no extension in the end of their name
> (IM_0465 for example) . Is it possible to change the format ?
>
> thanks ,
>
> Antoine
>
>
>
have you visually verified the talairach failed with tkregister2? If you
bring up the orig.mgz does it show properly (that is, is the view it calls
coronal actually coronal, etc...)?
On Tue, 4
May 2010, Antoine Leflon wrote:
> Hi all ,
>
> I've used data from another Doctor , freesurfer told m
My files are dicoms and have no extension in the end of their name
(IM_0465 for example) . Is it possible to change the format ?
thanks ,
Antoine
Talairach is about orientation. What is the format of your file?
Hi all ,
I've used data from another Doctor , freesurfer told me the FOV was
330 so I put the flag -cw256 in the command recon-all but the
Talairach just failed ...
I got this error message . Can someone explain please ?
_
Hello All,
I ran recon-all on a subject and got the following error
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#
#...@# Talairach Failure Detection Thu Nov 19 16:17:54 EST
Andrew,
The automatic failure detection has detected this failure. For the
talairach transform, it is sometimes conservative. First, check the
talairach transform to make sure it looks ok (fix it if it does not).
Then re-run recon-all with -notal-check
doug
Andrew Jahn wrote:
Hi,
I got
Hi,
I got the following error when trying to run recon-all on an MP-RAGE
T1-weighted image:
Fri Apr 10 16:25:01 EDT 2009
talairach_avi done
\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
#
#...@# Talairach Failure Detection Fri Apr 10 1
Nick,
I thought I would send your very precise fix to the list in case anyone
else just might run into the a similar issue.
I'd also like to thank you and Bruce profusely for all your great
help!
The longitudinal subject ran through successfully last night.
Sky
At 04:01 PM 4/17/2008, Nick Schman
Its possible that the alignment must be performed manually, at the very
least confirmed. Use tkregister2 to do this:
tkregister2 --s -fstal
More instructions are here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Nick
On Wed, 2008-02-27 at 20:19 +1100, wanlin wrote:
> -
>
-
Hi,
we met some errors as below when we run "recon-all -subjid SUBNAME
-autorecon1". Similar questions have been asked in
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06452.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06739.html
But the answer seems not
Mike,
Can you send me the input files for that subject? That is, the files
found in this directory of yours:
/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri/orig
If so, you can upload them to me via the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
N
Hello,
Thought that this might be of interest:
We've found a case for which the talairach.xfm is grossly wrong (checked
using tkregister2) but the automatic-failure detection of version 4.0.1
indicated no problems.
#
[EMAIL PROTECTED] Talairach Failure
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