Hi Michele,
Does $FREESURFER_HOME/mni/bin/nu_correct exist for you? This error usually indicates that you have not configured the freesurfer environment correctly. Have you sourced the SetUpFreeSurfer script?
Best,
Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Michele Valotti <michele.valotti@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, October 7, 2020 at 2:44 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 5.3.0 recon-all error
External Email - Use Caution
Hi, thank you for getting back to me so quickly, I can confirm that it does not run through on any scan and I have tried to run the command as you suggested.
This is the error I am getting:
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux ian-System-Product-Name 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 10 12:50:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Wed 7 Oct 16:46:17 BST 2020
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.1081
/home/michele/spd_processing/freesurfer2016/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=7.92, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.22236e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 4.65661e-10, -1)
k_ras = (7.82893e-09, 1, -4.65661e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1081/nu0.mnc...
--------------------------------------------------------
Iteration 1 Wed 7 Oct 16:46:18 BST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.1081/nu0.mnc ./tmp.mri_nu_correct.mni.1081/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1081/0/ -iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct
I am assuming I am missing the MNI tools, so I have tried to download them from
http://bic-mni.github.io/ but all the downloads failed, do you have a recommended way to download and install what I need to run my script?
Thank you again,
Michele
On Tue, 6 Oct 2020 at 15:59, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: