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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