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Hi,
I've been processing some 3T MRI scans through Freesurfer and recently
implemented the use of the -3T flag for nu-correction. I have processed
about 200 scans and the majority of them have gone through with out an
issue. However there are a handful
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Hm, that's not the error I thought you were getting. nu_correct is on your PATH
and your setup looks good.
I've never seen such an error, sorry.
Best,
Tim
> On April 4, 2019 at 9:40 AM Sevan Harootonian
> wrote:
>
>
> External Email - U
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Hi Tim,
I'm running freesurfer on linux. And the exact error is:
> ncvarput: ncid 5: Protocol error
> miicv_put: MINC package entry point
> nu_estimate_np_and_em: crashed while running mincmath (termination
> status=768)
> nu_correct: crashed while ru
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Dear Sevan,
Which version of FreeSurfer are you running on which system (Mac, Linux?), and
what is the exact command line and error message?
In case it is about nu_correct not being found: it should be in
$FREESURFER_HOME/mni/bin/nu_correct, and if
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Hello Freesurfers,
I'm running recond-all and getting ERROR: nu_correct. I see a lot of people
online have had this problem but I've failed to found a solution. Any
suggestions?
I'm running freesurfer on a virtual machine and I've attached
my recon-al
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Dear Freesurfer Experts,
I am having trouble with recon-all (Freesurfer 6.0). After running a shell
script on my subjects I get the following error:
Iteration 1 Fri Apr 20 13:22:37 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.14731/nu0.mn
I had the same problem with one server. The freesurfer version
is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
The system is openSUSE13.2 for both servers. But one works well (A), while
another one showed this problem (B). I found the kernel is somehow
different, though I am not sure
What version of freesurfer are you using? My guess is 5.3 or earlier?
With pre v6.0 versions of freesurfer, the Talairach transform step will
fail at the mri_nu_correct.mni command on newer Linux distributions that
come with perl version 5.22 (and higher) due to an incompatibility with
the mni
Dear Freesurfer Developers,
I was trying to use the recon-all -autorecon1 -subjid bert and got an error.
When I checked I found the error was coming while executing the below command:
nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc
./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mr
Sounds like it ran out of memory. Is that possible?
Bruce
On Jan 20, 2013, at 4:14 AM, Andrea Tateo wrote:
> Hi freesurfer experts,
>
> my jobs are finished with this output
>
> Processing:.Done
> Killed
> ERROR: nu_correct
>
>
Hi freesurfer experts,
my jobs are finished with this output
Processing:.DoneKilledERROR:
nu_correct
Can you help me?
endless thanks
Andrea ___
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Freesurfer@nmr.mgh.ha
Stefan,
Centos4 on VMWare on WindowsXP? Sounds interesting, and hope it can be
made to work.
What if you type:
nu_correct
Does it return something like this?
nu_correct, version 1.10
Usage: nu_correct [-help] [options] in.mnc out.mnc
If not, then please send me the error message. nu_
Hi freesurfers,
the script crashed when running "recon-all -s bert -all" to test a newly
installed CentOS 4 version (v3.0.3) on a Windows XP system with VMware and
Fedora Core 4. The path for both nu_correct (and nu_estimate_np_and_em:
see second error message) seem to be correct
(/mnt/d/Freesurfe
Ok. Sorry about the hassle.
On Wed, 2005-08-24 at 12:34 -0400, Keyma Prince wrote:
> Ok it look good now
>
> thanks
>
> Keyma Prince
> Massachusetts Institute of Technology
> Department of Brain and Cognitive Sciences
> NE20-392
> Cambridge, MA 02139
>
> On Wed, 24 Aug 2005, Nick Schmansky wrot
I get the same error.
Here is output you asked for:
[miracle:STRUCS] (nmr-std-env) cat /etc/redhat-release
CentOS release 4.1 (Final)
[miracle:STRUCS] (nmr-std-env) uname -a
Linux miracle 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686
athlon i386 GNU/Linux
[miracle:STRUCS] (nmr-std-env)
Kayma,
Can you give it a try now?
Also, can you type the following for me?
cat /etc/redhat-release
uname -a
This will tell me the machine OS and type. Unfortunately, I can't login
to miracle.
Nick
On Wed, 2005-08-24 at 11:40 -0400, Keyma Prince wrote:
> this is on miracle. I opened a ne
this is on miracle. I opened a new terminal window and here is the output
from nu_correct
[miracle:STRUCS] (nmr-std-env) nu_correct
Can't locate MNI/Startup.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5
/usr/lib/perl5/site_perl/5.8.5/i386-linux- thre
Keyma,
Hi, on which machine does this occur? If you start a new shell, and
type:
nu_correct
What does it display?
Nick
On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote:
> I just tried to run the following command and I got an error which has
> appeared before on the freesurfer list af
I just tried to run the following command and I got an error which has
appeared before on the freesurfer list after the MINC toolkit was rebuilt.
Can you let me know if this has happened again and what I can do about it?
thanks,
-Keyma
Command: recon-all -stage1 -subjid Y24_031905a_STRUC
Error
ok, it is working now. thanks! margaret
On Fri, 17 Jun 2005, Nick
Schmansky wrote:
Try it now.
I have recently rebuilt the MINC toolkit, but it seems I overlooked its
dependencies, and just now reverted the path back to where it was (and
will leave it that way).
Sorry for the hassle.
O
Try it now.
I have recently rebuilt the MINC toolkit, but it seems I overlooked its
dependencies, and just now reverted the path back to where it was (and
will leave it that way).
Sorry for the hassle.
On Fri, 2005-06-17 at 16:32 -0400, Margaret Duff wrote:
> Hi, I have just recently gotten
Hi, I have just recently gotten an error when running recon-all-nmr. I
am on the computer troy and my command line is recon-all-nmr -stage1
-subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER.
I tried resetting my LANG to C and en_US and neither made a difference.
It seems like
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