New subject: nu_correct problem (fwd)

17 Jan 2013


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---------- 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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Re: [Freesurfer] nu_correct problem (fwd)