Hallo, now I use cc...

Actually I gave you wrong info - I DID rename file patient.mgz to 001.mgz and not orig.mgz as I wrote before, sorry.

I attach recon-all.log file with errors from my last run. It is about nu_correct.

Thanks for help, Petr 

---------- Původní zpráva ----------
Od: Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu>
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

On Thu, 17 Jan 2013, Louis Nicholas Vinke wrote:

> Please remember to cc the list.
>
> ---------- Forwarded message ----------
> Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET)
> From: zach.petr@post.cz
> To: Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu>
> 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-v5.1.0-full.vdi, Documentation)
>
>  
>
> I´ll send recon-all.log file later on I have it on another PC.
>
>  
>
> Orig.mgz file  - thats also problem. What I did: when running recon-all
> -subjid name -autorecon1 I get
> error: no /mri/orig/orig.mgz file. I looked into patients /mri directory
> and this path and file is
> not there. So that I created directory /orig in /mri and copied there
> converted patient.mgz file there
> and renamed it to orig.mgz. So that I have
> /subject/patient/mri/orig/orig.mgz. Maybe thats what is
> wrong? How do you get normally orig.mgz file?
>
>  
>
> Thanks, Petr
>
>  
>
>
>  
>
> ---------- Původní zpráva ----------
> Od: Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu>
> Datum: 16. 1. 2013
> Předmět: Re: [Freesurfer] nu_correct problem
>
>
> 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 prior to the
> mri_nu_correct.mni step to see if it looks reasonable?
> -Louis
>
> On Wed, 16 Jan 2013, zach.petr@post.cz wrote:
>
> >
> >
> > 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
> >
> >
> >
>
>
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