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

Hi Bruce

here's the output

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # 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

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # nu_correct -version

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # which nu_correct/home/freesurfer/mni/bin/nu_correct

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri #

1st command: No output 2nd command: No output 3rd Command : freesurfer has never been installed on this machine before and there is no freesurfer entries in the home directory

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 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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