Ok - thank you! I will speak to the person who generated the files then.
On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve
wrote:
> I don't know how you (or someone else) generated the nifti files in the
> first place, so I can't help there. If you did not generate them, then
> talk to the person
I don't know how you (or someone else) generated the nifti files in the
first place, so I can't help there. If you did not generate them, then
talk to the person who did. I do not really recommend trying to do it by
hand. You can get AP and SI correctly, but you'll never know whether
they are L
Ah, I see - how would I be able to do either of those? And would I have to
check the geometry of each scan individually? Not sure how that works, but
I have a substantially large dataset.
Thank you for your response!
On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve
wrote:
> That means that geom
That means that geometry information (ie, what is left and right,
anterior or posterior) is not part of the nifti file. Without that
information, the anatomical analysis cannot be done. You will either
have to fix it yourself (ie, imbed that info into the file) or, better,
recreate the file wit
Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a
problem with the talairach registration. I've encountered this error before
here and there, but I've been receiving the same error for every scan that
I've been trying to run, and I'm not
the nifti file does not have the needed information in it. where did you
get it from?
On 9/5/17 8:42 PM, Ariana Vajdi wrote:
Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a
problem with the talairach registration. I've encountere
Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a
problem with the talairach registration. I've encountered this error before
here and there, but I've been receiving the same error for every scan that
I've been trying to run, and I'm not
Dear Experts,
according to the log, Vasudev is using version 5.3-HCP. Therefore I expect that
he is running FreeSurfer inside HCP pipeline scripts. The problem is that the
use of 6.0 version with HCP pipeline scripts is not currently recommended.
see
http://www.mail-archive.com/freesurfer@nmr.
This error is due to an incompatibility between the version of perl
shipped with ubuntu16 and the MINC tools shipped with freesurfer. This
issue has been fixed in freesurfer version 6.0, which I recommend you
download and install.
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
> I
It was actually mri_nu_correct.mni. this is our script that calls some
MNIC programs. What version of MINC are you using?
On 02/16/2017 01:01 PM, Dev vasu wrote:
> Dear FreeSurfer Developers,
>
> I am incurring Talairach registration error when i was running recon-all -s
>
> Error :
>
> recon-al
Dear FreeSurfer Developers,
I am incurring Talairach registration error when i was running recon-all -s
Error :
recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017
Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
Platform: Ubuntu 16.04
recon-all log
On 4/26/15 12:03 AM, Paul Dhami wrote:
Greetings FS experts,
I'm currently getting myself familiar with FS, and thus was going
through the processing of a few subjects. I have one subject whose
anatomical is not aligned with the horizontal/x axis, as seen right
after reconstruction of the r
sorry, I meant when registering two volumes from the same person (eg, T1
and fMRI). In that case, you might not really expect any scaling so you
should be careful. Nothing to do with the tal reg.
doug
On 08/10/2012 11:05 AM, Alexandra Tanner wrote:
> Thanks Doug! What do you mean by registering
Thanks Doug! What do you mean by registering to an individual? Is editing
the talairach registration for each individual subject not the same thing?
Thanks,
Alex
> Hi Alex, it is fine to scale the brain for the tal registration. It is
> when registering to an individual that one must be very car
Hi Alex, it is fine to scale the brain for the tal registration. It is
when registering to an individual that one must be very careful with
scaling.
doug
On 08/10/2012 08:51 AM, Alexandra Tanner wrote:
> Hi Doug,
>
> I'm currently looking into doing surface edits on past data and I heard
> someo
Hi Doug,
I'm currently looking into doing surface edits on past data and I heard
someone mention that one should never scale the brain when editing the
talairach registration. I was wondering if this was true, or if it's okay
to scale the brain so long as you check the scaling in all 3 dimensions
thanks Bruce :)
-Mojdeh
On 07/20/2012 04:27 PM, Bruce Fischl wrote:
> Hi Mojdeh
>
> it's really hard to say how much you should correct. In general we
> don't do that much. A couple of control points or a few voxels added
> to the wm.mgz can have a big effect if you are experienced. Mostly
> j
Hi Mojdeh
it's really hard to say how much you should correct. In general we don't
do that much. A couple of control points or a few voxels added to the
wm.mgz can have a big effect if you are experienced. Mostly just see if the
?h.white and pial surface are visually accurate, and if not see i
Hi Bruce,
Thank's for the reply! I'm not concerned about hippocampal volume for
now, mostly needing cortical thickness for my project! Yes, I am using
v5.1. So in case of cortical thickness I shouldn't worry too much about
Talairach registration? could you please tell me what are the main
thin
Hi Mojdeh
it won't affect any individual thickness measures, *but* will affect the
estimated total intracranial volume (eTIV). We don't typically use eTIV for
thickness correction, but do for things like hippocampal volume. Are you
using version 5.1? If so, that's the problem. Nick has a fix fo
Hi all,
Sorry for re-posting this but it seems it didn't get through!
I've just started to do cortical thickness analysis on some subjects and
I'm noticing some miss-registrations, more specifically the Talairach
image is smaller than the target image no matter what subject I look at!
I just w
Dear All,
Did someone already figured out a solution for this problem?
I get exactly the same error every time I run recon_all
There seems to be no answer on the mailing list yet
Thank you
Kind regards
Gregor
Hi Avi,
do you have any advise for Dana?
thanks
Bruce
On Tue, 30
Dear all,
I have a problem running Freesurfer on images having a relatively tight FOV.
While running talairach_afd, the registration of the template to the image
fails. Checking the registration (as explained on
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) reveals that
the templa
Hello,
I am a new freesurfer user and am interested in the subcortical volumetric
segmentation procedure that is used, particularly relating to the hippocampus.
I am finding it difficult to decipher exactly what freesurfer does in relation
to Talairach registration, I've read that there is an
Dear All,
In two of my subjects talairach registeration is giving me wrong results in the
sense instead of taking my input image to talairach space the talairach image
is registered to my input image. This happens just only in two subjects out of
14 subjects. Can anyone please tell me how to
Okay thanks very much.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thu 11/19/2009 3:30 PM
To: Rajagopalan, Venkateswaran
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] talairach registration-result
tkregister2 applies the transform to
aran
>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Thu 11/19/2009 12:43 PM
> To: Rajagopalan, Venkateswaran
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] talairach registration-result
>
> Hi Venkateswar
aligned almost
closely. So what is this image i looked at?
Thanks
venkateswaran
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thu 11/19/2009 12:43 PM
To: Rajagopalan, Venkateswaran
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] talairach
Hi Venkateswaran,
we don't apply the tal xform,just compute it (in
mri/transforms/talairach.xfm), so there is no volume "after talairach".
cheers,
Bruce
On Thu, 19 Nov 2009, Rajagopalan, Venkateswaran wrote:
> Dear Freesurfer Users,
>
> Could anyone please tell me what is the name of the image
Dear Freesurfer Users,
Could anyone please tell me what is the name of the image file after talairach
registration for instance like nu.mgz (after intensity correction).
Thanks
venkateswaran
===
P Please consider the environment before printing this e-mail
the final tal coords are the average of the corresponding surface regions,
where the correspondence is established using spherical registration. Does
that make sense?
On
Wed, 21 Jan 2009, Lucia Garrido wrote:
Many thanks for your e-mail, Bruce. Would you mind just giving me a bit
more detail
Many thanks for your e-mail, Bruce. Would you mind just giving me a bit
more detail about this, or let me know where I can find this information?
As I understand, the registration between individuals in Freesurfer
doesn't depend on the talairach registration. Is that right?
And how do individual t
Hi Lucia,
we almost never use the talairach except for reporting purposes.
cheers,
Bruce
On Tue, 20 Jan 2009, Lucia Garrido wrote:
Dear freesurfers,
I'm having some troubles deciding whether the output from the Tailarach
registration is good or not. I don't have hugely distorted brains as ca
Dear freesurfers,
I'm having some troubles deciding whether the output from the Tailarach
registration is good or not. I don't have hugely distorted brains as can
be seen in the tutorials. But though they seem roughly aligned, there are
some cases in which it seems it could benefit from changing t
Cameron,
If a bad talairach alignment prevents the creation of the surfaces (the
files in the subjects surf directory), then just exclude the '--surf
orig' flag from the tkregister2 cmd line. Use the 'Compare' button to
switch between the template (the blurry image) and your subject. It is
a lot
Does the lh.orig surface exist for that subject?
Cameron Ellis wrote:
Hi,
Hopefully this is something simple. When I try to check the talairach
transform for my subjects I type:
tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
and then I get this error:
subject = SM1C2_autorecona
Hi,
Hopefully this is something simple. When I try to check the talairach
transform for my subjects I type:
tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
and then I get this error:
subject = SM1C2_autoreconall
Reading lh surface orig
MRISread(/space/troy/3/users/retrievalnewest/SM
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