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 nicks@nmr.mgh.harvard.eduwrote:
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.
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 nicks@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@nmr.mgh.harvard.edu
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Nick Schmansky -
Susan Kuo