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