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The image quality is quite good. GM and WM contrast is excellent. There are
no scanning artifacts. The only remarkable finding is that this individual
has moderate brain atrophy, enlarged ventricles, and large white matter
signal abnormalities (hypointe
The first thing to do is to check your input data to make sure that
something is not really wrong. Eg, a large artifact or unusual anatomy.
On 1/17/19 5:35 AM, Daniel Ferreira wrote:
>
> External Email - Use Caution
>
> Thanks Greve. Yes, I mean that the moveable is completely black. How
External Email - Use Caution
Thanks Greve. Yes, I mean that the moveable is completely black. How should
I continue from here? If the registration is so far off that it is out
of the field of view, what should I do next?
Thanks
Dani
El mié., 16 ene. 2019 a las 22:54, Greve, Doug
when you say it does not load, do you mean that the moveable is
blank/black? The terminal output indicates that it is being loaded. It
is probably the case that the registration is so far off that it is out
of the field of view
On 1/16/19 11:30 AM, Daniel Ferreira wrote:
>
> External Em
External Email - Use Caution
Hi Greve,
Thanks for your quick reply.
I mean that tkregister2 loads the target volume (I think the original T1 it
is) but it does not load the moveable volume as stated in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview: "You
What do you mean that the tal volume does not load as a mov volume? Can you
send the terminal output from tkregister2?
On 1/16/19 10:01 AM, Daniel Ferreira wrote:
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Dear Bruce, Martin, and experts,
I posted an issue a few days ago. I have been looking throug
External Email - Use Caution
Dear Bruce, Martin, and experts,
I posted an issue a few days ago. I have been looking through the archives
but can not figure out the solution myself. I was wondering if you would
have any suggestion on how to fix the issue described further down?
T
External Email - Use Caution
Dear experts,
I am processing some data and one of my cases failed. I checked the
recon-all.log and found the following:
*#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET*
*/home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri*
Dear FS developers and expert users,
I am preprocessing with freesurfer 6.0 recon-all a set of pre defaced
subjects and the results are generally good, but the Talairach
transform QA measure are terribly bad and exactly the same on all defaced:
#
Hi Bruce,
Thanks so much.
So, how would I check if it actually failed or not?
How would I turn off the checking?
How would I manually correct it?
Would running without it be essentially the same as turning off the checking
(procedurally)?
Best,
Fred
> On Sep 14, 2016, at 15:59, Bruce Fisch
Hi Fred
have you checked the transform to see if it actually failed? If not, you
can just turn off the checking. If it did, you can manually correct it
(or run without it)
cheers
Bruce
On Wed, 14 Sep 2016, Uquillas, Federico D'Oleire wrote:
> Dear fellow FreeSurfer users,
>
> I can't get a su
Dear fellow FreeSurfer users,
I can't get a subject to recon-all all the way through without crashing,
regardless of the FS version used (deleted and started from scratch several
times).
It always fails with a Talairach transform fail error.
Wondering if anybody else has experienced this issue
Dear Doug,
As I mentioned in a previous email, I'm currently working with T1 DICOM
files from the Clinical PACS System that I'd like to pull into the
freesurfer stream to get cortical thickness. I've unpacked the data,
converting the DICOM files to mgz format, and successfully ran the first
recon-
not really, sorry.
On Sun, 1 Jul 2012, Andrew R. Dykstra wrote:
Thanks Bruce. I'll give that a try. But it seems strange to me that after
processing different subjects with autorecon1 that the transform info would
be missing from the header of some subjects but not others. Can you think
of an
Thanks Bruce. I'll give that a try. But it seems strange to me that after
processing different subjects with autorecon1 that the transform info would
be missing from the header of some subjects but not others. Can you think
of any reason why this might happen?
Cheers,
Andy
On Sun, Jul 1, 2012
Hi Andrew
try running:
mri_add_xform_to_header -c \
$SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm \
$SUBJECTS_DIR/$subject/mri/orig.mgz \
$SUBJECTS_DIR/$subject/mri/orig.mgz
or whatever volume (instead of orig.mgz) you were viewing in tkmedit. This
gets done automatically during the rec
Dear Freesurfers,
I am experiencing a strange issue when processing some, but not all,
subjects with the recommended recon stream. After autorecon1, which
includes Talairach registration step, I cannot see Talairach coordinates in
the tkmedit interface ('none' appears in the text box where the co
addendum: i mistakenly said that talairach.xfm is used in the
skull-strip stage... it is not. so beyond really bad talairach
failures, the only critical reason to redo the talairach.xfm is if the
ICV calculation (which itself is pretty rough) is valuable to you (for
correcting volume stats by hea
Andy,
I'll answer the last first: that error message (the one in ALL CAPS)
can be ignored. It originates in the bowels of some fortran code in the
VNL library we use. A real error detected at the level of our code
would exit if there was a problem with the minimization.
Per the talairach.xfm,
Hello Freesurfer Experts-
We recently reran several subjects from scratch through the stable
Freesurfer 5.0 pipeline who had previously been processed with the stable
4.5 pipeline. We used tkregister2 for QA of the 5.0 data and noticed that
the talairach transform was off (misaligned) for th
Hello,
I am fairly new to freesurfer, and recently encountered an error while running
recon-all (-autorecon1 -autorecon2) during Talairach Failure Detection:
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***Fp=0.0001, pv
Hi Lena,
no, not at this time. Sorry.
Bruce
On Thu, 8 Jul 2010, Lena Palaniyappan wrote:
Dear Bruce
We are trying to obtain a good contrast in 7T for thickness measurements
using freesurfer by piloting different sequences, is there anyway we can
process the T2*s in the pipeline?
On 08/07/20
Dear Bruce
We are trying to obtain a good contrast in 7T for thickness measurements
using freesurfer by piloting different sequences, is there anyway we can
process the T2*s in the pipeline?
On 08/07/2010 17:07, "Bruce Fischl" wrote:
> Hi Lena,
>
> -notal-check will disable the error detectio
Hi Lena,
-notal-check will disable the error detection, not the tal itself, so
won't help in cases where the xform is truly wrong. The image you sent
looks PD/T2* weighted, which won't work for the talairaching we use (or for
many of our analysis steps).Do you have a T1-weighted image?
cheer
well that certainly looks wrong. What does the original image look like?
On
Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach
step
The tkmedit displays normal coronal, sagittal positions for the target.
If I use tkregister2 t
I am trying to reconstruct some 7T images but they repeatedly fail Talairach
step
The tkmedit displays normal coronal, sagittal positions for the target.
If I use tkregister2 the moveable appears odd please see the attached
The error message is
#...@# Talairach Failure Detection Thu Jul 8 10:
Hi Corey,
something is very strange with that volume. Is it really only 77 slices? It
doesn't show properly in tkmedit, which means that the direction cosines
are probably messed up. The voxel sizes may be wrong too, as it looks very
odd. Do you have dicoms for it?
Bruce
On
Tue, 12 May 200
When trying to perform an auto recon on MRI_1.nii in
/space/annecy/12/users/adykstra/cashlab/MRI/BW10/mri/, I get the
following error during autorecon1:
---
Michelle,
Which version of freesurfer is installed? I think the libg2c dependency
was removed in the newest version.
Nick
On Mon, 2008-08-18 at 11:28 -0500, Michelle W. Voss wrote:
> Hello,
>
> This is my first time trying to use freesurfer on our data. We
> collect siemens dicom images, so I
Hello,
This is my first time trying to use freesurfer on our data. We collect
siemens dicom images, so I first manually reconstructed to .mgz format and
tried running the recon-all script. I've posted the log below.
Any ideas for fix?
thanks,
Michelle
mri_convert -it siemens_dicom -ot mgz
ONR
get volume that you want
your subject to match.
Can you send your command line.
Thanks,
Jenni
-Original Message-
From: Jackie_rwth [mailto:[EMAIL PROTECTED] Sent: Tuesday,
May 01, 2007 3:02 AM
To: Bruce Fischl
Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
your command line.
Thanks,
Jenni
-Original Message-
From: Jackie_rwth [mailto:[EMAIL PROTECTED] Sent:
Tuesday, May 01, 2007 3:02 AM
To: Bruce Fischl
Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.x
d.edu
Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in
mri/transforms dir, and also when I ran autorecon1 and put the -
notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz
EMAIL PROTECTED]
Sent: Tuesday, May 01, 2007 3:02 AM
To: Bruce Fischl
Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in
mri/transforms dir, and also when I ran autorecon1 and pu
that you want
your subject to match.
Can you send your command line.
Thanks,
Jenni
-Original Message-
From: Jackie_rwth [mailto:[EMAIL PROTECTED]
Sent: Tuesday, May 01, 2007 3:02 AM
To: Bruce Fischl
Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach tran
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in
mri/transforms dir, and also when I ran autorecon1 and put the -
notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in another
orietat
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the
mri/transforms dir.
When you say "after this step, the orientation of the target volume is
mixed up" do you mean after applying the tal transform? The orientation of
all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz)
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with
tikmedit. But after I fixed the Talairach transform by using mri_convert
T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it
in tkregister2, which looks quite fine), then I ran recon-all -subjid
Hi,
I'm a little confused, so please correct me if I've made the wrong
assumptions. It sounds like your problem is becuase your orig volume is
in the wrong orientation when you view it in tkmedit (ie., the coronal
view in tkmedit does not show a coronal view, but shows the sagital view).
It
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final
objective funciton value is fine, ca.0.06)
So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and
it looked pretty fine with tkregister2.
Then I runed recon-all -subjid -autore
Hi Lars,
definitely trust your eyes more than the objective function! If the xforms
are reasonable everything should work fine, but if you care about talairach
averaging or coords for reporting you should adjust them.
cheers,
Bruce
On Fri, 9 Dec 2005, Lars M. Rimol wrote:
Hi,
We have 15 o
Hi Lars,
You should be able to just move on with -autorecon2 as normal. The only
need to re-do anything would be if your poor talairach caused some other
step to be wrong (i.e., the skull strip failed or the normalization failed
because the talairach was wrong). If those are fine, then continue
Hi,We have 15 out of 16 data sets with Final Objective Function value 0.1. We also find some deviations from the talairach (or MNI) volume when we visually inspect the images (fixed vs. movable) in tkregister2. But we are unsure how large the deviations must be for it to be a problem, so we rely on
depends why you needed to improve the talairach. If it's just for
reporting purposes and the filling/intensity normalization all worked
fine then you don't need to.
cheers,
Bruce
On Thu, 8 Dec 2005, Lars M. Rimol wrote:
Hi,
After having redone mri_convert with an edited brain.mgz as input fil
Hi,
After having redone mri_convert with an edited brain.mgz as input file, in order to improve the talairach transform, and after having changed the file names (brain.xfm -> talairach.xfm), should we then go to autorecon2? (or do we need to re-run some more scripts from autorecon1?)
-- yours,
Hi Michele,
we typically use tkregister2 or the mni register program to fix it
manually.
cheers,
Bruce
On Wed, 7 Sep 2005, Michele Perry wrote:
I ran recon-all -stage1 -nomotioncor -subjid
It exited with errors during mri_fill:
mri_fill: could not find corpus callosum
No such file or direc
I don't know why it failed, but you should try fixing it with
tkregister2 --fstal --s
then run with -notalairach
given how bad it is, you might be better starting from scratch, in which
case you should add --regheader to the cmd
doug
Michele Perry wrote:
I ran recon-all -stage1 -nomotio
I ran recon-all -stage1 -nomotioncor -subjid
It exited with errors during mri_fill:
mri_fill: could not find corpus callosum
No such file or directory
INFO: Modifying dst c_(r,a,s), using the transform dst
INFO: Modifying dst c_(r,a,s), using the transform dst
find_cutting_plane:seed point not in
the final objective function value is not a great indicator of failure
of the talairaching procedure. it's a better indicator of success. if it
is low(<.1), you can be confident it is correct. if it is high, that does
not mean it is incorrect, but that you should check it. certain brains
(with
Hi Tracy,
I don't know what the problem could be, but you can always by-pass the
automatic talairaching with manual with tkregister2. When you run
recon-all just make sure to include -notalairach as the last option.
doug
Tracy Wang wrote:
Hi All,
It seems that my talairach transforms
Hi All,
It seems that my talairach transforms are still suspect, FOF values falling between the 13-.17 range. I've tried Xiao Han's suggestion to skull strip first, but it the final objective function value is still high. Once the transform is applied on the image in native space, it does look a
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