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.edumailto:dgreve@mgh.harvard.edu> wrote:
My guess is it is a problem with the install of the MNI tools. Does it run all the way through on other subjects? What happens when you run this command?
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
On 10/6/2020 9:16 AM, Michele Valotti wrote:
External Email - Use Caution I am using freesurfer 5.3.0 (unfortunately this is the version I have to use) and I am encountering an error in the process. I have attached the recon-all.log file. Any pointers to identify the error would be very helpful,
Thank you, Michele
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