Petr why do you keep trying to name your input files something.mgz, when you
were in wisconsin i told you the inputs always need to be 001.mgz
at this point i think you need to get invited to upload one of your data sets
to ugh and see if there is a problem
with the data or is it a problem with
--
Od: Louis Nicholas Vinke
Datum: 17. 1. 2013
Předmět: Re: [Freesurfer] nu_correct problem (fwd)
"Hi Petr,
Try renaming /subject/patient/mri/orig/orig.mgz to
/subject/patient/mri/orig/001.mgz and rerunning recon-all. The orig.mgz
file is created later on in the recon-all stream.
-Louis
O
.
-- Forwarded message --
Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET)
From: zach.p...@post.cz
To: Louis Nicholas Vinke
Subject: Re: Re: [Freesurfer] nu_correct problem
Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web
page
(freesurfer-Virtualbox-linux-x86-stable-pub
Please remember to cc the list.
-- Forwarded message --
Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET)
From: zach.p...@post.cz
To: Louis Nicholas Vinke
Subject: Re: Re: [Freesurfer] nu_correct problem
Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web
Hi Petr,
Can you provide us with some more details? Which version of FreeSurfer
are you using and on what platform? Could you attach a copy of the
recon-all.log file for one of these cases so we can read the full error
reported?
Have you tried looking at the orig.mgz which is generated prio
Dear members,
when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu
_correct. This happens for DICOM but also IMA file type. I tried several
brains. Do you have any idea what is wrong?
Thanks much, Petr Zach
___
Freesurfer mail
ot;Nick
> Schmansky [ni...@nmr.mgh.harvard.edu]
> Gesendet: Dienstag, 10. Juli 2012 14:07
> Bis: Christopher Bell
> Cc: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] nu_correct problem
>
> Chris,
>
> This is an unusual error. I dont know why nu_correct would b
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Nick
Schmansky [ni...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 10. Juli 2012 14:07
Bis: Christopher Bell
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer]
Chris,
This is an unusual error. I dont know why nu_correct would be found for
some subjects but not others, if its being run on the same platform. I
can only think this is a network issue. Is it replicable? nu_correct can
be run from the command line.
The intensity normalization issues in v5
I believe this post slipped through the cracks. Anyone have any thoughts
on this nu_correct error. Some subjects ran fine, so it seems to be an
intermittent
problem and not an installation problem.
Also, is this possibly related to the avi_talairach/intensity normalization
issues
being discussed i
Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on
most of my subjects, but for about 10 subjects, I got an error:
nu_correct: Command not found
I can see on the archive that several others have run into this problem,
but I couldn't figure out from the archives what the
Hi Reddy,
the nu isn't smoothing them, it's what we call the "conform" process -
interpolating to 1mm isotropic. Your voxels are 1.25x1.25x1.2, which is
almost 90% larger than 1mm iso, so when we upsample them there is a bunch
of interpolation.
cheers
Bruce
On Fri, 13 Nov 2009, Mr k hanimire
Tao,
Which freesurfer distribution was installed, and on what kind of platform?
Was there an MNI installation already on the system and are there
environment variables pointing to it? In particular, what are
MNI_DATAPATH and MNI_PERL5LIB and PERL5LIB set to in your environment?
They should poin
>Hi Bruce:
>>
>> I installed the new version of freesurfer. I found that nu_correct does
>> not work properly, the error message is
>> spawn: exec of nu_estimate_np_and_em failed: No such file or directory
>> nu_correct: crashed while running nu_estimate_np_and_em (termination
>> status=65280)
>>
>
I'm having problems with recon-all. It used to work but recently, every
time I've used it, I get a nu_correct error. I don't think we have had
any freesurfer upgrades since the last time recon-all worked. Here's the
log. Anyone know what's wrong?
ip07:mperry[12] setenv SUBJECTS_DIR
ip07:mper
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