Susan,

there appear to be two problems here. the first and main problem is the one:

nu_correct: Command not found.

nu_correct is a script which has as its first line:

#!/usr/bin/perl -w

so can you check that you have perl installed at /usr/bin/perl?

better yet, run this script:

fixup_mni_paths

which does the checking for you and attempts to fix the scripts.

the other problem appears to be the fact that mri_nu_correct.mni doesnt exit upon finding the error that the files are missing. this is bad, although in looking at the script, it ought to. the next release will contain a double check. from the looks of your script, it appears that you are running recon-all with a subject that had its data already processed, so nu.mgz existed already, so it just used that and continued on. so the results are correct (assuming nu.mgz was decent to begin with), but resolving the nu_correct issue is the important thing to do.

Nick

On Wed, 2013-01-09 at 11:00 -0500, Susan Kuo wrote:

Hi, I'm currently in the process of verifying that my install of Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be 4 errors after running recon-all -s bert -autorecon1. The last line I included here states that the command completed without error, so I'm not sure if I should be concerned thatnu_correct wasn't found, or that there were loading errors, and a mincREAD() error. Could you help me identify what I need to do to correct these issues? I've included the standard output for this command as a text file here. There appear to be 4 issues:

***ISSUE 1: cannot find nu_correct ************************* nu_correct: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing.

***ISSUE 2: No such file or directory error******************** cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file or directory mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25253/ones.mgz mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc

***ISSUE 3: Loading error****************************** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25253/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open file

***ISSUE 4: Loading error****************************** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc ./tmp.mri_nu_correct.mni.25253/nu2.mnc mul mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc

****This is the last line to standard output, and it seems reassuring********************** recon-all -s bert finished without error at Tue Jan 8 17:49:19 EST 2013

I appreciate whatever help you can give me, and thank you very much for your time! The attached is a text file.

Best, S Kuo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer