Can you send the log file?
On 2/10/2021 10:26 AM, Bohorquez Montoya, Luisa wrote:
External Email - Use Caution
Hello Freesurfer
I have been trying to run this subject 3 times (with different
walltime) and I am having the same error. Would you mind please to
explain me what I am doi
Hi Emily
no log file attached...
cheers
Bruce
On Tue, 6 Jun 2017, Emily Rogers wrote:
> Hello,
>
> I am trying to implement using Freesurfer segmentation in my analysis for MEG
> data. I am trying to segment this structural MRI (1400composite.dcm) and I
> keep getting errors. I have attached t
Hello,
I am trying to implement using Freesurfer segmentation in my analysis for MEG
data. I am trying to segment this structural MRI (1400composite.dcm) and I keep
getting errors. I have attached the log file. Any help is appreciated.
Thank you,
Emily
Emily E. Rogers, MSc
Wake Forest Graduat
Hello Maura,
Here at the Center we stopeed active development of the stable6 branch
and focused all our development on the dev version. A new stable6 will
be cut soon from dev soon, but in the meantime I have linked the two
together (stable6=dev). So feel free to resubmit your job, as the bug
Hi Maura
we are in the process of updating stable6. The existing version has a bug
that causes these crashes. Hopefully we'll have something usable soon
sorry
Bruce
On Wed, 16 Dec 2015, Hamel, Maura K. wrote:
Hi Freesurfer experts,
I’m looking for some help with some recons I tried running y
Hi,
I got this error while running recon-all : 'imgreg_4dfp
/opt/freesurfer-530/average/711-2C_as_mni_average_305
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR:
mpr2mni305 execution abo
Hi,
I got this error while running recon: 'imgreg_4dfp
/opt/freesurfer-530/average/711-2C_as_mni_average_305
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR:
mpr2mni305 execution aborted
Xiao
: [Freesurfer] recon error- too many arguments?
Hi Mia, I think the problem is that you have a space in the path to the
dicom. Even though you put a backslash there, I think it is still
causing the problem
doug
On 06/15/2012 01:13 PM, Borzello, Mia wrote:
> Yes! I attached a screen shot. Tha
nks!
>
>
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, June 15, 2012 11:33 AM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon error- too many arguments?
>
> Hi Mia
>
> can you send us the actual command and sc
Yes! I attached a screen shot. Thanks!
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, June 15, 2012 11:33 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon error- too many arguments?
Hi Mia
can you
Hi Mia
can you send us the actual command and screen output?
thanks
Bruce
On Fri, 15 Jun 2012,
Borzello, Mia wrote:
> Hi,
>
> I'm trying to run a recon, but I keep getting the error: too many arguments
> for the following command:
> econ-all -autorecon1 -autorecon2 -autorecon3 -subject _Su
Hi,
I'm trying to run a recon, but I keep getting the error: too many arguments for
the following command:
econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i
[path to dicom]
Any help on this would be excellent!
Thanks,
M
___
Have you tried including the flag -cw256 with the recon-all command?
On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` wrote:
> Hi!,
>
> I am new to FreeSurfer and I am having some difficulty with the T1
> reconstruction. My MRI files were Par Rec and converted to nii. I
> successfully conver
Hi Michele,
this means that the computed talairach transformation was deemed to be
unlikely and therefore possibly wrong. This usually occurs when the input
volume is in the incorrect orientation. Did you convert to analyze format
at any time? If you bring the orig.mgz up in tkmedit are the ori
Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the
University of Padua with a degree in Mathematics.
I'm trying to use FreeSurfer for analyze a 3D image MRI, DICOM format (I
have NIFTI too) to calculate brain volume.
I ran
recon-all -autorecon1 -autorecon2 -subjid <..."file
Hi Rodrigo, first check the talairach registration to see whether it
really failed or not -- the automatic checker is often a bit
conservative. If it did, then you can fix it by hand. If it did not,
then you can re-run recon-all with -notal-check.
doug
Rodrigo Zepeda wrote:
> Hi,
>
> I'm getti
Hi,
I'm getting an error trying to run a reconstruction.
I'm working on multnomah and my subjects directory
is: /autofs/space/multnomah_002/users/Cashlab/
*I'm using the following command:*
[multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject
MG15_SurferOutput -i
MG15/MG
Thanks. I tried running it on oct and I'm getting another error earlier on
recon process.
The subjects directory is: /homes/11/rzepeda/Recon
I'm using the following command:
[oct:~/Recon] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject
MG25_SurferOutput -i
MG25/MRI/1.3.12.2.1107.5.2.30
Looks like that is a pretty weak computer. Can you run it on a stronger
computer?
Rodrigo Zepeda wrote:
> Hi,
>
>I'm getting an error trying to run a reconstruction.
>
> I'm working on multnomah and my subjects directory
> is: /autofs/space/multnomah_002/users/Cashlab/
>
> I'm using the foll
Hi,
I'm getting an error trying to run a reconstruction.
I'm working on multnomah and my subjects directory
is: /autofs/space/multnomah_002/users/Cashlab/
I'm using the following command:
[multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject
MG25_SurferOutput -i
MG25/MR
can you send us the recon-all command line?
On Wed, 12 Nov 2008, Alexa
Nardelli wrote:
Hi guys, I also have another question: I am getting the following error
message when I run recon-all with a few of my images:
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR:
Hi guys, I also have another question: I am getting the following
error message when I run recon-all with a few of my images:
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status
Ilana,
use:
tkregister2 --s (subjid) --fstal
note that the talairach alignment can fail for a number of reasons. a
catastrophic one would be if the direction cosines in the input file are
all wrong (coronal, saggital, horizontal wrong). or it could be that
the subject was just scanned in an
Hi there,
I am new to free surfer, and am trying to analyse brains of kids ages 8-11.
running recon1 i get the following error message:
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)
Looking at past mailings seems you re
gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz:
No such file or directory
mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz,
-1): read error
I went into my subjects directory and to the subject that I ran with
the error and received the above.
--
Frederick
it is in the mri dir:
/Users/frederickpowell/freesurfer/subjects/011106RJ/mri/nu.mgz
On Thu, 1 Jun
2006, Frederick Powell wrote:
gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz:
No such file or directory
mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz
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