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.p...@post.cz
To: Louis Nicholas Vinke <vi...@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 <vi...@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.p...@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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