Susie, I'm sorry, but I'm at a loss here as to this 'nu_correct: Command not found' problem. If you've confirmed that typing:
/usr/bin/perl -v returns a perl version number, then I dont know what else to try, as I dont have an Ubuntu 12.04.1 system to experiment with. Nick On Thu, 2013-01-10 at 14:05 -0500, Susan Kuo wrote: > Thank you, Nick. I tried using fixup_mni_paths, but received a poor > result. I copied the stdout below: > > > *** > yocto/j/dti7/Susie/freesurfer/subjects> su > Password: > root@yocto:/j/dti7/Susie/freesurfer/subjects# fixup_mni_paths > fixup_mni_paths: command not found > root@yocto:/j/dti7/Susie/freesurfer/subjects# cd $FREESURFER_HOME/bin > root@yocto:/usr/local/freesurfer/bin# fixup_mni_paths > fixup_mni_paths: command not found > root@yocto:/usr/local/freesurfer/bin# ./fixup_mni_paths > Using perl '/usr/bin/perl' > Patching autocrop...(original file saved to autocrop.old) > Patching field2imp...(original file saved to field2imp.old) > Patching imp2field...(original file saved to imp2field.old) > Patching make_template...(original file saved to make_template.old) > Patching mritoself...(original file saved to mritoself.old) > Patching mritotal...(original file saved to mritotal.old) > Patching nu_correct...(original file saved to nu_correct.old) > Patching nu_estimate...(original file saved to nu_estimate.old) > Patching nu_estimate_np_and_em...(original file saved to > nu_estimate_np_and_em.old) > Patching nu_evaluate...(original file saved to nu_evaluate.old) > Patching resample_labels...(original file saved to > resample_labels.old) > Patching sharpen_volume...(original file saved to sharpen_volume.old) > Patching xfmtool...(original file saved to xfmtool.old) > done. > Here are the changes: > diff autocrop autocrop.old > diff field2imp field2imp.old > diff imp2field imp2field.old > diff make_template make_template.old > diff mritoself mritoself.old > diff mritotal mritotal.old > diff nu_correct nu_correct.old > diff nu_estimate nu_estimate.old > diff nu_estimate_np_and_em nu_estimate_np_and_em.old > diff nu_evaluate nu_evaluate.old > diff resample_labels resample_labels.old > diff sharpen_volume sharpen_volume.old > diff xfmtool xfmtool.old > done. > Note: not all systems will require a patch, > and may not show any differences. > Now a test of the MNI tool 'nu_correct'... > nu_correct: Command not found. > A version number and usage message should have been displayed. > *** > > > I double-checked that /usr/bin/perl exists, so that's ok. I've been > crawling the forums, but I can't find a good answer for what appears > to be a simple problem. Can I fix this manually? > > > Thanks! > Susie > > On Wed, Jan 9, 2013 at 4:29 PM, Nick Schmansky > <ni...@nmr.mgh.harvard.edu> wrote: > 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 > > > > > 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
