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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@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 >> >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
