Subject: Re: [Freesurfer] recon-all error
Looks like it ran out of memory
Cheers
Bruce
On Apr 16, 2014, at 2:22 PM, Boric, Katica A.
kbo...@mgh.harvard.edumailto:kbo...@mgh.harvard.edu wrote:
Hello Freesurfers!
This case of recon-all -s MGHXXX_SurferOutput exited with ERRORS. Attach is
the recon
, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: recon-all exited w/errors
oh, it's only 62 slices? So is it not whole brain? Or are they thick
slices? Either way that is probably a show stopper
On Mon, 6 Jan 2014,
Boric, Katica A. wrote:
Hi Bruce!
Thank you very much
, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: FW: recon-all exited w/errors
what is the slice thickness? Usually we recommend no dimension be thicker
than 1.5mm or so
On Mon, 6 Jan 2014, Boric, Katica A. wrote:
Hi Bruce!
So it is the whole brain! Unfortunately
Happy New Year freesuerfers!
I run into this error while doing recon-all :
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
Greetings Freesurfers!
recon-all -s XXX_SurferOutput exited with ERRORS
These are the errors in the log:
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
I would really appreciate any advice!
Thank you very
. The physical computer is an Intel(R) Core
i5 CPU 2.67GHz with 8GB of RAM
I will just do it again!
Thanks again,
Katica
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, November 11, 2013 2:33 PM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Greetings Freesurfers!
recon-all -s XXX_SurferOutput exited with ERRORS
These are the errors in the log:
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
I would really appreciate any advice!
Thank you very
Dear freesurfer experts:
I am trying to process an MRI using recon-all -autorecon1 -autorecon2
-autorecon3
and exited with errors. Apparently the encoded image data is not supported
(below you can see the recon-all.log)
Is there a way to process this study?
Thank you very much for your
shell?
The path to the freesurfer home is: usr/local/freesurfer
Thank you very much,
Katica
From: Z K [zkauf...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 12:41 PM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
with a tcsh shell?
The path to the freesurfer home is: usr/local/freesurfer
Thank you very much,
Katica
From: Z K [zkauf...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 12:41 PM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 03, 2013 12:03 PM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in MRI processing
setenv FREESURFER_HOME /usr/local/freesurfer
On Tue, 3 Sep 2013, Boric,
Katica A. wrote:
Hi everyone!
I wrote you
/freesurfer/subjects2
and nothing happened. Am I doing something wrong?
Thanks,
Katica
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 03, 2013 12:08 PM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re
]
Sent: Tuesday, September 03, 2013 3:05 PM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in MRI processing
Hi Katicia
can you be more detailed about what you did? What command did you issue
after you moved the dicoms? Where did you move them to? In general
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 10:51 AM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in MRI processing
Hi Katica
does /usr/local/freesurfer/subjects/fsaverage
...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 11:04 AM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in MRI processing
can you run:
cd /mnt/hgfs/Linux_Share/subjects
ln -s /usr/local/freesurfer/subjects/fsaverage
and tell us what it says?
Bruce
On Fri
this:
drwxr-xr-x. 7 root root 4096 Oct 23 2012
/usr/local/freesurfer/subjects/fsaverage
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 11:15 AM
To: Boric, Katica A.
Subject: Re: [Freesurfer] error in MRI processing
how
Hi everyone!
I am new to freesurfer, and I was processing and MRI using recon-all
-autorecon1 -autorecon2 -autorecon3 command and I have a message that the
processing was exited with ERRORS. When checking the recon-all. log it appears
that these are the error (highlighted in yellow):
#@# BA
Hi Bruce!
Thanks for your fast response.
/usr/local/freesurfer/subjects/fsaverage does exists!
Thanks again,
Katica
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 10:51 AM
To: Boric, Katica A.
Cc: freesurfer
, Katica A.
Subject: Re: [Freesurfer] error in MRI processing
how about:
On Fri, 30 Aug 2013, Boric,
Katica A. wrote:
This comes out:
drwxrwxrwx. 1 root root 0 Aug 29 11:10 /mnt/hgfs/Linux_Share/subjects
From: freesurfer-boun...@nmr.mgh.harvard.edu
/2013 11:41 AM, Boric, Katica A. wrote:
Hi Bruce this comes out from ls -ald $FREESURFER_HOME/subjects/fsaverage
drwxr-xr-x. 7 root root 4096 Oct 23 2012
/usr/local/freesurfer/subjects/fsaverage
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent
, 2013 11:11 AM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in MRI processing
that probably means you don't have write access to the subject directory.
Can you run:
ls -ald /mnt/hgfs/Linux_Share/subjects
On Fri, 30 Aug 2013, Boric, Katica A.
wrote
Hello!
I am new to free surfer and Linux and I am having installing free surfer. I am
using Fedora on a VMware workstation
I successfully (I think) downloaded it and installed it following the
instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall). But now
I am stuck trying to
From: Boric, Katica A.
Sent: Monday, August 26, 2013 4:02 PM
To: Douglas N Greve
Subject: RE: [Freesurfer] How do we obtain the .license file from registration
e-mail and put it in the Freesurfer home directory?
Hi Doug!
Thanks for getting back so fast
file in a text editor (eg, emacs, gedit, etc). Do not do
this on a windows machine. Cut and paste those 3 lines into the file.
doug
On 08/26/2013 04:06 PM, Boric, Katica A. wrote:
From: Boric, Katica A.
Sent: Monday, August 26, 2013 4:02 PM
To: Douglas
and put it in the Freesurfer home directory?
How did FS get there in the first place? If you installed it, then you
must have permission. If you did not, find who did and have him/her copy it
doug
On 08/26/2013 04:29 PM, Boric, Katica A. wrote:
Thanks Doug
I created a file using gedit but I can't
and put it in the Freesurfer home directory?
How did FS get there in the first place? If you installed it, then you
must have permission. If you did not, find who did and have him/her copy it
doug
On 08/26/2013 04:29 PM, Boric, Katica A. wrote:
Thanks Doug
I created a file using gedit but I
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