Hi Bruce
Just checked the actual location of the file is
/UK_Biobank_MRI/freesurfer/mni/bin/nu_correct
i.e. FREESURFER_HOME/mni/bin
Dave
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 04 December 2015 14:04 To: Freesurfer support list Subject: Re: [Freesurfer] Path Problem
Hi Dave
that is pretty puzzling. The nu1.mnc is the output of the command that is failing, so I don't see why it complains that it doesn't exist. The same command:
nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc ./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2
works fine for me. Can you try it from the command line (from the mri dir)? If it fails, can you run:
nu_correct -version
and
which nu_correct?
cheers Bruce
On Fri, 4 Dec 2015, LIEWALD David wrote:
Hi Bruce
Yes the dir is writable and the echo command does create the test.dat in the subdir.
I have attached a recon-all log as requested
Many Thanks
Dave ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 04 December 2015 13:36 To: Freesurfer support list Subject: Re: [Freesurfer] Path Problem
HI David
can you write to that dir? For example, does
echo test > ./tmp.mri_nu_correct.mni.24767/test.dat
work properly (from the mri dir)? Also, please send us the entire recon-all.log so we can have a look
cheers Bruce
On Fri, 4 Dec 2015, LIEWALD David wrote:
Environment : Opensuse 13.2 Freesurver Version 6 (Beta)
Hi I hope you can help with this problem
I'm using the version 6 Beta due to problems with license authentication. Freesurfer runs but bails out with a file not found error :
Iteration 1 Fri Dec 4 09:38:57 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc ./tmp.mri_nu_correct.mni.24767/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2
ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux
on examination of the file structure a directory named "tmp.mri_nu_correct.mni.24767" has been created under the "mri"directory and nothing has been created under the "tmp" directory in the subject root. I am guessing that this is the cause of the error.
any advice on correcting this would be extremely useful
Dave Liewald
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